| Next changeset 1:52225f471c57 (2018-01-22) |
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Commit message:
planemo upload for repository https://github.com/shao-lab/MAnorm/tree/master/galaxy-tool |
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added:
manorm.xml test-data/H1_vs_K562_H3K4me3_all_MAvalues.xls test-data/H1hescH3k4me3Rep1_peaks.xls test-data/H1hescH3k4me3Rep1_reads.bed test-data/K562H3k4me3Rep1_peaks.xls test-data/K562H3k4me3Rep1_reads.bed test-data/output_dir/output_figures/sample1_vs_sample2_MA_plot_after_normalization.png test-data/output_dir/output_figures/sample1_vs_sample2_MA_plot_before_normalization.png test-data/output_dir/output_figures/sample1_vs_sample2_MA_plot_with_P-value.png test-data/output_dir/output_figures/sample1_vs_sample2_read_density_on_common_peaks.png test-data/output_dir/output_filters/sample1_M_above_1.0_biased_peaks.bed test-data/output_dir/output_filters/sample1_M_below_-1.0_biased_peaks.bed test-data/output_dir/output_filters/sample1_vs_sample2_unbiased_peaks.bed test-data/output_dir/output_tracks/sample1_vs_sample2_A_values.wig test-data/output_dir/output_tracks/sample1_vs_sample2_M_values.wig test-data/output_dir/output_tracks/sample1_vs_sample2_P_values.wig test-data/output_dir/sample1_vs_sample2_all_MAvalues.xls |
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| diff -r 000000000000 -r 9cd4a30cb4f8 manorm.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/manorm.xml Mon Jan 22 04:03:44 2018 -0500 |
| [ |
| @@ -0,0 +1,132 @@ +<tool id="manorm" name="MAnorm" version="1.0"> + <description>Quantitative comparison of ChIP-Seq samples</description> + <requirements> + <requirement type="package" version="1.1.2">manorm</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + manorm --p1 $p1 --p2 $p2 --r1 $r1 --r2 $r2 $s --name1 sample1 --name2 sample2 -o output_dir + #if $s1 + --s1 $s1 + #end if + + #if $s2 + --s2 $s2 + #end if + + #if $settings.advanced == "on" + #if $settings.w + -w $settings.w + #end if + + #if $settings.d + -d $settings.d + #end if + + #if $settings.n + -n $settings.n + #end if + #end if + + #if $m + -m $m + #end if + + #if $p + -p $p + #end if + ]]></command> + <inputs> + <param argument="--p1" type="data" format="tabular,bed" label="Peaks file of sample 1" /> + <param argument="--p2" type="data" format="tabular,bed" label="Peaks file of sample 2" /> + <param argument="--r1" type="data" format="bed" label="Reads file of sample 1" /> + <param argument="--r2" type="data" format="bed" label="Reads file of sample 2" /> + <param argument="--s1" type="integer" value="100" optional="true" label="Reads shift size of sample 1" + help="This value is used to shift reads towards 3' direction to determine the precise binding site. Set as half of the fragment length." /> + <param argument="--s2" type="integer" value="100" optional="true" label="Reads shift size of sample 2" + help="Same as 'Reads shift size of sample 1'" /> + <param argument="-m" type="float" value="1.0" optional="true" label="M-value (log2 fold change) cutoff" /> + <param argument="-p" type="float" value="0.01" optional="true" label="P-value cutoff" /> + <conditional name="settings"> + <param name="advanced" type="select" label="Show advanced options"> + <option value="on">Yes, show advanced options.</option> + <option value="off" selected="true">No</option> + </param> + <when value="on"> + <param argument="-w" type="integer" value="1000" optional="true" label="Width of the window to calculate read densities" + help="Windows with unified length of 2*width centered at peak summit/midpoint are used to quantify the binding signal. + This should match the typical length of peaks, a value of 1000 is recommended for sharp histone marks like H3K4me3 and H3K9/27ac, + and 500 for transcription factors or DNase-Seq." /> + <param argument="-d" type="integer" value="500" optional="true" label="Summit-to-summit distance cutoff for common peaks" + help="Only overlapped peaks with summit-to-summit distance less than than this value are considered as real common peaks of two samples when fitting M-A normalization model." /> + <param argument="-n" type="integer" value="10" optional="true" label="Number of simulation to test the enrichment of peak overlap between two samples" /> + </when> + <when value="off"> + </when> + </conditional> + <param argument="-s" type="boolean" truevalue="-s" falsevalue="" optional="true" label="Full output" + help="By default, MAnorm will write the comparison results of unique and merged common peaks in a single output file. + With this option on, two extra files which contains the results of the original(unmerged) peaks will also be outputted." /> + </inputs> + <outputs> + <data name="main_output" format="tabular" label="MAnorm (main result)" from_work_dir="output_dir/sample1_vs_sample2_all_MAvalues.xls" /> + <data name="sample1_output" format="tabular" label="MAnorm (sample1 result)" from_work_dir="output_dir/sample1_MAvalues.xls"> + <filter>s == True</filter> + </data> + <data name="sample2_output" format="tabular" label="MAnorm (sample2 result)" from_work_dir="output_dir/sample2_MAvalues.xls"> + <filter>s == True</filter> + </data> + <data name="sample1_biased_peaks" format="bed" label="MAnorm (sample1 biased peaks)" from_work_dir="output_dir/output_filters/sample1_M_above_*_biased_peaks.bed" /> + <data name="sample2_biased_peaks" format="bed" label="MAnorm (sample2 biased peaks)" from_work_dir="output_dir/output_filters/sample1_M_below_*_biased_peaks.bed" /> + <data name="unbiased_peaks" format="bed" label="MAnorm (unbiased peaks)" from_work_dir="output_dir/output_filters/sample1_vs_sample2_unbiased_peaks.bed" /> + <data name="m_value_track" format="wig" label="MAnorm (M values track)" from_work_dir="output_dir/output_tracks/sample1_vs_sample2_M_values.wig" /> + <data name="a_value_track" format="wig" label="MAnorm (A values track)" from_work_dir="output_dir/output_tracks/sample1_vs_sample2_A_values.wig" /> + <data name="p_value_track" format="wig" label="MAnorm (P values track)" from_work_dir="output_dir/output_tracks/sample1_vs_sample2_P_values.wig" /> + <data name="ma_plot_before" format="png" label="MAnorm (MA plot before normalization)" from_work_dir="output_dir/output_figures/sample1_vs_sample2_MA_plot_before_normalization.png" /> + <data name="ma_plot_after" format="png" label="MAnorm (MA plot after normalization)" from_work_dir="output_dir/output_figures/sample1_vs_sample2_MA_plot_after_normalization.png" /> + <data name="ma_plot_with_p_value" format="png" label="MAnorm (MA plot with P values)" from_work_dir="output_dir/output_figures/sample1_vs_sample2_MA_plot_with_P-value.png" /> + <data name="read_density_plot" format="png" label="MAnorm (Read density plot)" from_work_dir="output_dir/output_figures/sample1_vs_sample2_read_density_on_common_peaks.png" /> + </outputs> + <tests> + <test> + <param name="p1" value="H1hescH3k4me3Rep1_peaks.xls" ftype="tabular" /> + <param name="p2" value="K562H3k4me3Rep1_peaks.xls" ftype="tabular" /> + <param name="r1" value="H1hescH3k4me3Rep1_reads.bed" ftype="bed" /> + <param name="r2" value="K562H3k4me3Rep1_reads.bed" ftype="bed" /> + <param name="s1" value="100" /> + <param name="s2" value="100" /> + <output name="main_output" file="H1_vs_K562_H3K4me3_all_MAvalues.xls"/> + </test> + </tests> + <help><![CDATA[ +What it does? +------------- + +MAnorm is a robust model for quantitative comparison of ChIP-Seq data sets. It uses the common peaks between two samples +to fit a rescaling model for normalization and infers the binding difference in all peak regions. + +Workflow of MAnorm: + - Classify peaks from given samples into unique/common peaks + - Take common peaks to fit a robust linear model to reflect the rescaling relationship between two samples + - Normalize all peaks with the fitted model + - Infer differential binding events by M-value (log2 fold change) + + +Documentation +------------- +To see the full documentation of MAnorm, please refer to: http://manorm.readthedocs.io/en/latest/ + + +Links +----- +The Python version of MAnorm is developed by ShaoLab_ at `CAS-MPG Partner Institute for Computational Biology, SIBS, CAS`_. + +GitHub: https://github.com/shao-lab/MAnorm + +.. _ShaoLab: http://bioinfo.sibs.ac.cn/shaolab/ +.. _CAS-MPG Partner Institute for Computational Biology, SIBS, CAS: http://www.picb.ac.cn/picb/indexeng.jsp + + ]]></help> + <citations> + <citation type="doi">10.1186/gb-2012-13-3-r16</citation> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/H1_vs_K562_H3K4me3_all_MAvalues.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/H1_vs_K562_H3K4me3_all_MAvalues.xls Mon Jan 22 04:03:44 2018 -0500 |
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| b'@@ -0,0 +1,847 @@\n+chr\tstart\tend\tsummit\tM_value\tA_value\tP_value\tPeak_Group\tnormalized_read_density_in_sample1\tnormalized_read_density_in_sample2\n+chr22\t17089331\t17090971\t355\t-0.77275\t4.22147\t0.0175888164449\tsample1_unique\t14.2718\t24.3837\n+chr22\t17600766\t17601507\t570\t1.57851\t3.24593\t0.00485157966614\tsample1_unique\t16.39501\t5.4895\n+chr22\t17601561\t17603428\t1126\t2.94106\t3.85712\t1.7362239646e-08\tsample1_unique\t40.15896\t5.2292\n+chr22\t17678919\t17681229\t1189\t3.41949\t4.19508\t6.15682960343e-13\tsample1_unique\t59.91416\t5.59964\n+chr22\t17737651\t17739303\t553\t2.92689\t2.29248\t0.00091552734375\tsample1_unique\t13.50971\t1.7765\n+chr22\t17741607\t17742657\t590\t2.11613\t2.58995\t0.0042724609375\tsample1_unique\t12.53609\t2.89163\n+chr22\t17744939\t17746309\t794\t1.94216\t2.94741\t0.00369644165039\tsample1_unique\t15.12109\t3.93491\n+chr22\t17746388\t17748139\t1072\t2.60893\t2.5222\t0.00091552734375\tsample1_unique\t14.18865\t2.32581\n+chr22\t17859935\t17861030\t198\t2.55944\t2.5\t0.00091552734375\tsample1_unique\t13.73438\t2.32992\n+chr22\t17861057\t17861822\t403\t2.71216\t2.19616\t0.00277709960938\tsample1_unique\t11.73089\t1.79015\n+chr22\t17915382\t17916720\t788\t2.16246\t2.32193\t0.0047607421875\tsample1_unique\t10.57921\t2.36313\n+chr22\t18404489\t18405788\t584\t1.57145\t2.78112\t0.0138854980469\tsample1_unique\t11.85025\t3.98725\n+chr22\t18592646\t18594259\t1266\t2.72675\t3.09984\t3.42726707458e-05\tsample1_unique\t22.05777\t3.33218\n+chr22\t18647168\t18647907\t552\t1.10468\t3.55817\t0.0161167234182\tsample1_unique\t17.27376\t8.03239\n+chr22\t18648072\t18649118\t393\t1.02225\t3.60473\t0.0232797116041\tsample1_unique\t17.33787\t8.53627\n+chr22\t18921129\t18924431\t2202\t2.24131\t4.50351\t5.44949123197e-08\tsample1_unique\t49.32219\t10.43136\n+chr22\t18957349\t18959277\t909\t1.41867\t4.59615\t0.000165141518873\tsample1_unique\t39.54669\t14.79272\n+chr22\t19136299\t19137531\t612\t1.12669\t2.90689\t0.0333251953125\tsample1_unique\t11.08268\t5.07548\n+chr22\t19273071\t19274301\t705\t-0.23592\t3.39232\t0.0840940475464\tsample1_unique\t9.67566\t11.39461\n+chr22\t19510337\t19512720\t750\t3.36377\t3.1496\t1.04657374322e-06\tsample1_unique\t28.47226\t2.76583\n+chr22\t19608751\t19609615\t602\t-1.11373\t3.54373\t0.0161167234182\tsample1_unique\t7.92749\t17.15545\n+chr22\t19962336\t19962994\t196\t-1.95946\t3.81741\t9.78546449915e-05\tsample1_unique\t7.1487\t27.80245\n+chr22\t20725303\t20727187\t707\t0.76083\t3.56593\t0.0389666557312\tsample1_unique\t15.41588\t9.09778\n+chr22\t20790009\t20793276\t2483\t1.87549\t4.06593\t7.96589040419e-05\tsample1_unique\t32.08162\t8.74334\n+chr22\t21310580\t21312984\t1139\t2.80007\t3.91724\t6.65552519763e-08\tsample1_unique\t39.8712\t5.72472\n+chr22\t21318520\t21320010\t627\t-0.00564\t4.22869\t0.0642926603177\tsample1_unique\t18.71172\t18.78501\n+chr22\t21385902\t21387790\t693\t1.18896\t3.96832\t0.00381633115467\tsample1_unique\t23.63413\t10.36638\n+chr22\t22279641\t22280445\t609\t0.21568\t2.97418\t0.0981903076172\tsample1_unique\t8.46799\t7.29213\n+chr22\t23487143\t23488439\t626\t-1.72312\t5.06464\t2.2771538717e-07\tsample1_unique\t18.41845\t60.80845\n+chr22\t23578975\t23579942\t559\t-0.92436\t3.78112\t0.0186544004828\tsample1_unique\t9.97931\t18.93915\n+chr22\t23583534\t23585842\t1538\t-0.13827\t5.38965\t0.039499347846\tsample1_unique\t39.96084\t43.98028\n+chr22\t23907486\t23909535\t730\t3.12739\t3.65189\t2.30261321121e-08\tsample1_unique\t37.15759\t4.25216\n+chr22\t24302548\t24304742\t1150\t4.01623\t2.78112\t2.02562659979e-07\tsample1_unique\t27.65053\t1.70883\n+chr22\t24320985\t24322905\t1007\t2.93401\t3.39232\t2.38185748458e-06\tsample1_unique\t29.02703\t3.7982\n+chr22\t24353252\t24354002\t309\t0.69714\t1.95345\t0.109375\tsample1_unique\t4.93148\t3.0417\n+chr22\t24550957\t24553548\t792\t2.73583\t3.62869\t1.58578404807e-06\tsample1_unique\t31.92479\t4.79249\n+chr22\t24819546\t24821142\t662\t1.22608\t3.69616\t0.00578929670155\tsample1_unique\t19.82433\t8.47445\n+chr22\t24889959\t24891411\t388\t3.21148\t2.79248\t1.50799751282e-05\tsample1_unique\t21.08609\t2.27638\n+chr22\t25392839\t25393613\t193\t2.02837\t2.26178\t0.008056640625\tsample1_unique\t9.68643\t2.37445\n+chr22\t25677590\t25680097\t1587\t5.42196\t3.41168\t2.70627026648e-19\tsample1_unique\t69.67939\t1.62529\n+chr22\t26564073\t26566978\t1751\t4.5006\t3.37073\t2.83106871279e-13\tsample1_unique\t49.21513\t2.17412\n+c'..b'9.50707\n+chr22\t45071889\t45074793\t1463\t-4.3139\t4.31468\t1.47408946887e-22\tsample2_unique\t4.46212\t88.74722\n+chr22\t45080448\t45081893\t1173\t-2.57857\t3.1427\t0.000111386179924\tsample2_unique\t3.61355\t21.58542\n+chr22\t45611346\t45612968\t630\t-3.44056\t2.5\t5.00679016113e-05\tsample2_unique\t1.7168\t18.63935\n+chr22\t45708465\t45711741\t1906\t-5.81794\t2.71313\t2.22044604925e-14\tsample2_unique\t0.87306\t49.25164\n+chr22\t45998587\t45999600\t443\t-2.50007\t2.88078\t0.000317096710205\tsample2_unique\t3.09673\t17.51859\n+chr22\t46014387\t46015177\t296\t-1.82075\t2.24593\t0.02685546875\tsample2_unique\t2.52373\t8.91543\n+chr22\t46034769\t46035377\t468\t-2.12268\t2.41645\t0.0111083984375\tsample2_unique\t2.55817\t11.14087\n+chr22\t46462688\t46464235\t1095\t-4.63266\t2.04373\t2.62260437012e-06\tsample2_unique\t0.82783\t20.53567\n+chr22\t46480103\t46483502\t2119\t-6.50267\t3.09984\t4.29099942762e-24\tsample2_unique\t0.90032\t81.63834\n+chr22\t46589567\t46590561\t575\t-3.53574\t2.08496\t0.000228881835938\tsample2_unique\t1.24582\t14.44832\n+chr22\t46630205\t46632040\t964\t-4.82782\t2.81468\t6.91215973347e-11\tsample2_unique\t1.32021\t37.49406\n+chr22\t46786198\t46787218\t556\t-2.17318\t2.69616\t0.00259399414062\tsample2_unique\t3.05161\t13.76326\n+chr22\t46851230\t46852461\t777\t-3.73263\t2.19616\t3.43322753906e-05\tsample2_unique\t1.25688\t16.70809\n+chr22\t46959098\t46960261\t566\t-1.12879\t3.45345\t0.0146124958992\tsample2_unique\t7.40785\t16.19914\n+chr22\t46999309\t47001409\t653\t-3.67385\t3.29248\t1.53449946083e-08\tsample2_unique\t2.74262\t35.00296\n+chr22\t47044982\t47046222\t699\t-3.31482\t2.42899\t0.000163078308105\tsample2_unique\t1.70714\t16.98748\n+chr22\t47047805\t47048545\t152\t-2.41588\t2.28493\t0.0047607421875\tsample2_unique\t2.10963\t11.25793\n+chr22\t47149605\t47151076\t715\t-2.67322\t3.19616\t6.5378844738e-05\tsample2_unique\t3.62894\t23.14727\n+chr22\t47330272\t47332573\t1362\t-4.26457\t2.96537\t4.58385329694e-09\tsample2_unique\t1.78149\t34.24105\n+chr22\t47732688\t47733415\t541\t-3.82033\t1.58496\t0.00146484375\tsample2_unique\t0.79818\t11.27554\n+chr22\t48026267\t48029425\t1483\t-6.48735\t3.75191\t9.4774232035e-38\tsample2_unique\t1.42231\t127.60889\n+chr22\t49447787\t49448819\t651\t-1.59848\t2.78112\t0.0138854980469\tsample2_unique\t3.95007\t11.96178\n+chr22\t49764635\t49765621\t465\t-5.74732\t1.54373\t2.62260437012e-06\tsample2_unique\t0.39779\t21.36815\n+chr22\t50048953\t50052069\t1968\t-4.68868\t4.11681\t2.45337003701e-23\tsample2_unique\t3.41638\t88.10488\n+chr22\t50097692\t50098812\t398\t-3.58788\t2.11441\t0.0001220703125\tsample2_unique\t1.24874\t15.01518\n+chr22\t50179678\t50180601\t294\t-4.01722\t1.69616\t0.00042724609375\tsample2_unique\t0.80527\t13.03908\n+chr22\t50200909\t50202776\t1122\t-4.80832\t2.80367\t6.91215973347e-11\tsample2_unique\t1.31906\t36.95839\n+chr22\t50328011\t50328960\t555\t-1.33519\t2.95943\t0.0236053466797\tsample2_unique\t4.89679\t12.35502\n+chr22\t50523560\t50524565\t327\t-2.17318\t2.69616\t0.00259399414062\tsample2_unique\t3.05161\t13.76326\n+chr22\t50543552\t50544765\t680\t-2.99928\t2.61441\t0.000163078308105\tsample2_unique\t2.1656\t17.31619\n+chr22\t50555334\t50558338\t634\t-3.45685\t3.16993\t3.17580997944e-07\tsample2_unique\t2.71604\t29.82303\n+chr22\t50606763\t50608437\t293\t-1.16075\t3.2539\t0.018482208252\tsample2_unique\t6.37986\t14.26369\n+chr22\t50679295\t50680533\t605\t-3.44056\t2.5\t5.00679016113e-05\tsample2_unique\t1.7168\t18.63935\n+chr22\t50707546\t50708451\t727\t-1.16264\t3.9915\t0.00607143592788\tsample2_unique\t10.63081\t23.79885\n+chr22\t50752385\t50753651\t824\t-2.50007\t2.88078\t0.000317096710205\tsample2_unique\t3.09673\t17.51859\n+chr22\t50756814\t50758035\t795\t-4.29001\t1.85022\t6.48498535156e-05\tsample2_unique\t0.81519\t15.94713\n+chr22\t50768593\t50770366\t746\t-4.69318\t3.57105\t2.05022630817e-16\tsample2_unique\t2.33668\t60.44872\n+chr22\t50936245\t50937827\t1085\t-3.40584\t3.39232\t2.82670953311e-08\tsample2_unique\t3.22523\t34.18378\n+chr22\t50977507\t50978750\t386\t-3.86263\t2.26958\t1.81198120117e-05\tsample2_unique\t1.26424\t18.39058\n+chr22\t51051823\t51052907\t310\t-2.57151\t2.66993\t0.000924110412598\tsample2_unique\t2.61023\t15.516\n+chr22\t51059873\t51061094\t486\t-1.86169\t3.529\t0.000701732933521\tsample2_unique\t6.05512\t22.0063\n+chr22\t51180653\t51181336\t514\t-3.09528\t1.83621\t0.002685546875\tsample2_unique\t1.22143\t10.43855\n' 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| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/H1hescH3k4me3Rep1_peaks.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/H1hescH3k4me3Rep1_peaks.xls Mon Jan 22 04:03:44 2018 -0500 |
| b |
| b'@@ -0,0 +1,584 @@\n+# This file is generated by MACS\n+chr\tstart\tend\tlength\tsummit\ttags\t\n+chr22\t16192293\t16193176\t884\t199\t16\t100.54\t25.73\t4.61\n+chr22\t17081410\t17082059\t650\t410\t13\t81.67\t18.31\t13.53\n+chr22\t17082917\t17084523\t1607\t1261\t42\t253.86\t24.64\t0.56\n+chr22\t17089331\t17090971\t1641\t355\t29\t165.45\t19.30\t0.90\n+chr22\t17565234\t17567384\t2151\t702\t98\t702.84\t29.79\t0.23\n+chr22\t17600766\t17601507\t742\t570\t10\t56.67\t12.87\t86.39\n+chr22\t17601561\t17603428\t1868\t1126\t83\t627.54\t50.07\t0.26\n+chr22\t17638646\t17641551\t2906\t705\t127\t800.27\t29.34\t0.21\n+chr22\t17651863\t17653756\t1894\t464\t56\t417.24\t34.31\t0.36\n+chr22\t17678919\t17681229\t2311\t1189\t120\t657.70\t17.99\t0.25\n+chr22\t17737651\t17739303\t1653\t553\t31\t137.23\t12.52\t1.28\n+chr22\t17741607\t17742657\t1051\t590\t26\t141.54\t19.71\t1.19\n+chr22\t17744939\t17746309\t1371\t794\t28\t120.54\t11.52\t2.02\n+chr22\t17746388\t17748139\t1752\t1072\t32\t77.52\t8.45\t17.87\n+chr22\t17847453\t17852425\t4973\t3188\t408\t3100.00\t56.33\t0.34\n+chr22\t17859935\t17861030\t1096\t198\t21\t66.48\t8.23\t38.59\n+chr22\t17861057\t17861822\t766\t403\t16\t82.30\t11.20\t13.08\n+chr22\t17915382\t17916720\t1339\t788\t21\t92.87\t14.74\t7.16\n+chr22\t18110239\t18112527\t2289\t1076\t288\t2945.43\t96.40\t0.35\n+chr22\t18120421\t18123144\t2724\t1533\t274\t3057.25\t108.40\t0.32\n+chr22\t18255229\t18258071\t2843\t1233\t114\t773.39\t35.20\t0.21\n+chr22\t18404489\t18405788\t1300\t584\t22\t82.86\t11.52\t12.67\n+chr22\t18482576\t18484870\t2295\t666\t88\t736.83\t36.45\t0.22\n+chr22\t18505809\t18507961\t2153\t1278\t87\t482.65\t26.15\t0.33\n+chr22\t18559632\t18562122\t2491\t1288\t244\t2632.51\t112.65\t0.30\n+chr22\t18592646\t18594259\t1614\t1266\t51\t368.39\t35.70\t0.42\n+chr22\t18631720\t18633637\t1918\t1251\t59\t432.59\t42.24\t0.34\n+chr22\t18647168\t18647907\t740\t552\t14\t77.22\t13.10\t18.17\n+chr22\t18648072\t18649118\t1047\t393\t21\t100.76\t20.34\t4.57\n+chr22\t18891536\t18892389\t854\t499\t12\t61.31\t11.42\t59.08\n+chr22\t18893072\t18895128\t2057\t386\t120\t1173.92\t66.21\t0.18\n+chr22\t18921129\t18924431\t3303\t2202\t128\t991.96\t57.67\t0.20\n+chr22\t18957349\t18959277\t1929\t909\t75\t552.68\t52.40\t0.30\n+chr22\t19107555\t19111309\t3755\t1595\t184\t1237.01\t49.29\t0.19\n+chr22\t19131061\t19132798\t1738\t857\t151\t1563.32\t92.31\t0.20\n+chr22\t19136299\t19137531\t1233\t612\t19\t91.25\t10.83\t7.76\n+chr22\t19156314\t19161213\t4900\t3480\t314\t2912.29\t82.14\t0.39\n+chr22\t19164556\t19167586\t3031\t2275\t129\t853.82\t37.12\t0.20\n+chr22\t19273071\t19274301\t1231\t705\t18\t71.10\t11.98\t27.87\n+chr22\t19277753\t19280319\t2567\t1097\t111\t718.05\t31.33\t0.23\n+chr22\t19417226\t19421025\t3800\t2997\t309\t2714.66\t49.29\t0.33\n+chr22\t19433817\t19436432\t2616\t1933\t228\t2564.28\t127.12\t0.28\n+chr22\t19464980\t19468852\t3873\t1323\t339\t3100.00\t98.85\t0.34\n+chr22\t19510337\t19512720\t2384\t750\t74\t434.48\t16.90\t0.33\n+chr22\t19608751\t19609615\t865\t602\t12\t57.03\t12.32\t83.63\n+chr22\t19702045\t19702752\t708\t439\t11\t60.10\t9.14\t64.87\n+chr22\t19705581\t19707008\t1428\t549\t27\t146.66\t18.10\t1.11\n+chr22\t19708838\t19712330\t3493\t1360\t72\t323.13\t18.78\t0.47\n+chr22\t19717979\t19718993\t1015\t593\t18\t84.08\t14.98\t11.80\n+chr22\t19742529\t19743902\t1374\t1140\t20\t66.26\t8.45\t39.13\n+chr22\t19743997\t19744970\t974\t568\t15\t62.16\t10.06\t55.24\n+chr22\t19750136\t19750811\t676\t388\t11\t52.92\t7.41\t100\n+chr22\t19840491\t19843572\t3082\t1514\t215\t1983.86\t53.57\t0.23\n+chr22\t19928568\t19930912\t2345\t1216\t61\t410.34\t36.45\t0.38\n+chr22\t19946046\t19947881\t1836\t711\t44\t278.51\t43.03\t0.53\n+chr22\t19962336\t19962994\t659\t196\t12\t59.32\t11.27\t68.27\n+chr22\t19973161\t19975135\t1975\t1023\t99\t854.84\t66.89\t0.20\n+chr22\t20003014\t20005623\t2610\t1648\t78\t506.27\t32.63\t0.31\n+chr22\t20008043\t20009686\t1644\t987\t87\t661.19\t34.72\t0.24\n+chr22\t20067700\t20069522\t1823\t676\t208\t2367.07\t100.14\t0.23\n+chr22\t20103238\t20107077\t3840\t2460\t310\t3100.00\t121.45\t0.34\n+chr22\t20118187\t20120574\t2388\t1685\t58\t322.21\t33.93\t0.47\n+chr22\t20254329\t20256628\t2300\t1122\t61\t409.96\t30.17\t0.38\n+chr22\t20285696\t20288769\t3074\t728\t93\t543.02\t28.36\t0.29\n+chr22\t20306368\t20308924\t2557\t1500\t153\t1345.22\t51.63\t0.19\n+chr22\t20377162\t20380577\t3416\t1170\t81\t521.95\t25.73\t0.30\n+chr22\t20423634\t20427628\t3995\t3502\t106\t702.75\t36.45\t0.23\n+chr22\t20427989\t20428968\t980\t289\t25\t171.71\t23.59\t0.88\n+chr22\t20460116\t20461654\t1539\t837\t33\t178.29\t16.67\t0.83\n+chr22\t20725303\t20727187\t1885\t707\t34\t152.56\t15.65\t1.04\n+chr22\t20'..b'\t52\t474.56\t45.03\t0.33\n+chr22\t46645267\t46647550\t2284\t710\t67\t453.22\t40.76\t0.33\n+chr22\t46663027\t46664655\t1629\t625\t61\t503.04\t35.20\t0.31\n+chr22\t46691355\t46694181\t2827\t1718\t209\t1837.58\t51.21\t0.21\n+chr22\t46730473\t46733311\t2839\t1325\t191\t1669.55\t47.88\t0.21\n+chr22\t46773767\t46774425\t659\t367\t10\t61.58\t10.72\t58.04\n+chr22\t46932543\t46935154\t2612\t1371\t61\t332.04\t20.61\t0.46\n+chr22\t46971660\t46972916\t1257\t683\t34\t236.25\t29.34\t0.58\n+chr22\t46973082\t46974444\t1363\t538\t39\t262.16\t34.25\t0.56\n+chr22\t47132758\t47135121\t2364\t601\t95\t810.00\t57.61\t0.22\n+chr22\t47157017\t47160018\t3002\t1096\t290\t2756.68\t69.23\t0.34\n+chr22\t47423356\t47424365\t1010\t358\t14\t57.89\t14.08\t75.09\n+chr22\t47485800\t47487685\t1886\t1269\t60\t334.49\t22.17\t0.46\n+chr22\t48074222\t48075110\t889\t412\t12\t61.37\t11.90\t58.87\n+chr22\t48635084\t48635738\t655\t301\t10\t61.83\t12.87\t56.92\n+chr22\t48765019\t48767195\t2177\t1271\t54\t222.66\t18.41\t0.61\n+chr22\t48884475\t48885110\t636\t406\t12\t73.69\t12.80\t22.96\n+chr22\t48885285\t48888080\t2796\t280\t129\t897.46\t28.87\t0.21\n+chr22\t48892275\t48893299\t1025\t607\t18\t108.79\t17.16\t3.05\n+chr22\t48970238\t48971533\t1296\t631\t16\t76.20\t21.44\t19.23\n+chr22\t48972091\t48973035\t945\t198\t22\t144.16\t27.88\t1.14\n+chr22\t49665632\t49666105\t474\t200\t10\t69.98\t14.40\t30.14\n+chr22\t49843835\t49845097\t1263\t321\t17\t85.70\t12.87\t10.74\n+chr22\t49906377\t49907496\t1120\t455\t19\t80.32\t11.27\t14.95\n+chr22\t49929667\t49931058\t1392\t442\t25\t106.22\t11.27\t3.48\n+chr22\t50025409\t50026900\t1492\t762\t40\t287.99\t40.74\t0.51\n+chr22\t50063785\t50065606\t1822\t582\t39\t182.12\t18.31\t0.82\n+chr22\t50118034\t50119126\t1093\t478\t17\t89.18\t13.69\t8.65\n+chr22\t50164642\t50165788\t1147\t458\t21\t115.37\t22.23\t2.39\n+chr22\t50219229\t50221284\t2056\t1269\t100\t888.96\t55.97\t0.21\n+chr22\t50241426\t50243736\t2311\t613\t51\t250.45\t15.65\t0.56\n+chr22\t50246070\t50247305\t1236\t756\t63\t556.97\t56.33\t0.30\n+chr22\t50247810\t50249523\t1714\t380\t103\t1037.42\t83.63\t0.19\n+chr22\t50310765\t50313512\t2748\t1201\t107\t637.58\t31.68\t0.26\n+chr22\t50329774\t50330590\t817\t154\t16\t95.87\t14.93\t5.89\n+chr22\t50353025\t50356517\t3493\t2341\t109\t673.51\t41.25\t0.25\n+chr22\t50364123\t50364817\t695\t376\t10\t51.32\t10.56\t100\n+chr22\t50437157\t50439204\t2048\t1244\t46\t192.94\t16.82\t0.77\n+chr22\t50496347\t50498533\t2187\t955\t54\t349.80\t30.17\t0.45\n+chr22\t50609115\t50610093\t979\t270\t25\t175.80\t26.15\t0.84\n+chr22\t50622927\t50624516\t1590\t1035\t39\t143.77\t14.08\t1.15\n+chr22\t50624549\t50625911\t1363\t485\t42\t303.27\t36.21\t0.49\n+chr22\t50628541\t50629492\t952\t678\t16\t83.11\t15.84\t12.47\n+chr22\t50637957\t50641004\t3048\t2443\t133\t766.46\t20.12\t0.21\n+chr22\t50681905\t50684748\t2844\t1211\t223\t2370.56\t82.61\t0.23\n+chr22\t50688543\t50690908\t2366\t915\t86\t522.71\t34.56\t0.30\n+chr22\t50698584\t50700071\t1488\t721\t24\t84.98\t8.96\t11.13\n+chr22\t50708623\t50710498\t1876\t476\t38\t185.09\t17.21\t0.81\n+chr22\t50731086\t50732274\t1189\t516\t25\t162.49\t25.73\t0.94\n+chr22\t50737898\t50738966\t1069\t407\t17\t62.17\t8.78\t55.23\n+chr22\t50744021\t50746159\t2139\t1499\t86\t723.29\t49.07\t0.23\n+chr22\t50764585\t50766555\t1971\t686\t72\t541.79\t32.50\t0.29\n+chr22\t50780547\t50782269\t1723\t914\t83\t724.52\t51.88\t0.23\n+chr22\t50911957\t50913464\t1508\t890\t60\t510.25\t43.49\t0.31\n+chr22\t50913501\t50914244\t744\t187\t21\t136.92\t22.70\t1.28\n+chr22\t50919075\t50920826\t1752\t1467\t65\t488.65\t35.20\t0.32\n+chr22\t50945046\t50947742\t2697\t936\t207\t2284.83\t83.63\t0.25\n+chr22\t50962861\t50965511\t2651\t1087\t123\t1021.94\t40.89\t0.20\n+chr22\t50968441\t50971303\t2863\t669\t78\t340.47\t15.16\t0.46\n+chr22\t50982556\t50983350\t795\t463\t10\t53.86\t10.72\t100\n+chr22\t51001098\t51002209\t1112\t476\t67\t524.80\t32.86\t0.30\n+chr22\t51019986\t51022635\t2650\t1847\t150\t1284.90\t45.37\t0.18\n+chr22\t51039077\t51039882\t806\t607\t12\t66.75\t16.09\t37.90\n+chr22\t51041943\t51042912\t970\t724\t17\t103.54\t17.16\t3.98\n+chr22\t51065429\t51067662\t2234\t962\t124\t1085.46\t52.98\t0.19\n+chr22\t51079737\t51081273\t1537\t947\t31\t108.37\t9.46\t3.10\n+chr22\t51111226\t51112598\t1373\t1054\t58\t441.23\t32.86\t0.33\n+chr22\t51113031\t51114747\t1717\t742\t48\t260.00\t28.16\t0.55\n+chr22\t51135273\t51135748\t476\t187\t10\t59.25\t10.24\t68.60\n+chr22\t51136188\t51136686\t499\t187\t11\t68.88\t14.08\t32.44\n+chr22\t51159009\t51159761\t753\t197\t12\t73.21\t12.87\t23.64\n+chr22\t51195313\t51196282\t970\t445\t14\t64.65\t13.66\t45.91\n+chr22\t51220706\t51223142\t2437\t1729\t175\t1667.69\t70.41\t0.21\n' |
| b |
| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/H1hescH3k4me3Rep1_reads.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/H1hescH3k4me3Rep1_reads.bed Mon Jan 22 04:03:44 2018 -0500 |
| b |
| b'@@ -0,0 +1,113352 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MAAAXX:5:75:294:1780\t0\t-\n+chr22\t51222412\t51222448\tSL-XBE_3_FC30CMAAAXX:5:6:132:821\t0\t-\n+chr22\t51222415\t51222451\tSL-XBE_3_FC30CMAAAXX:5:78:1617:880\t0\t-\n+chr22\t51222419\t51222455\tSL-XBE_3_FC30CMAAAXX:5:15:1740:1430\t0\t+\n+chr22\t51222430\t51222466\tSL-XBE_3_FC30CMAAAXX:5:30:722:1450\t0\t+\n+chr22\t51222431\t51222467\tSL-XBE_3_FC30CMAAAXX:5:94:1664:1759\t0\t+\n+chr22\t51222433\t51222469\tSL-XBE_3_FC30CMAAAXX:5:41:1388:1247\t0\t+\n+chr22\t51222433\t51222469\tSL-XBE_3_FC30CMAAAXX:5:24:402:1246\t0\t+\n+chr22\t51222439\t51222475\tSL-XBE_3_FC30CMAAAXX:5:68:205:371\t0\t+\n+chr22\t51222441\t51222477\tSL-XBE_3_FC30CMAAAXX:5:98:400:1078\t0\t-\n+chr22\t51222460\t51222496\tSL-XBE_3_FC30CMAAAXX:5:30:793:507\t0\t+\n+chr22\t51222461\t51222497\tSL-XBE_3_FC30CMAAAXX:5:76:736:1482\t0\t-\n+chr22\t51222478\t51222514\tSL-XBE_3_FC30CMAAAXX:5:17:1562:778\t0\t-\n+chr22\t51222488\t51222524\tSL-XBE_3_FC30CMAAAXX:5:11:769:1215\t21\t+\n+chr22\t51222490\t51222526\tSL-XBE_3_FC30CMAAAXX:5:4:184:620\t27\t-\n+chr22\t51222496\t51222532\tSL-XBE_3_FC30CMAAAXX:5:23:1679:469\t27\t+\n+chr22\t51222497\t51222533\tSL-XBE_3_FC30CMAAAXX:5:64:1114:810\t27\t-\n+chr22\t51222501\t51222537\tSL-XBE_3_FC30CMAAAXX:5:64:1630:1641\t26\t+\n+chr22\t51222502\t51222538\tSL-XBE_3_FC30CMAAAXX:5:59:1091:1247\t0\t+\n+chr22\t51222536\t51222572\tSL-XBE_3_FC30CMAAAXX:5:30:717:958\t27\t-\n+chr22\t51222545\t51222581\tSL-XBE_3_FC30CMAAAXX:5:4:1370:1349\t17\t-\n+chr22\t51222565\t51222601\tSL-XBE_3_FC30CMAAAXX:5:13:152:378\t0\t-\n+chr22\t51222595\t51222631\tSL-XBE_3_FC30CMAAAXX:5:96:1361:1726\t0\t-\n+chr22\t51222596\t51222632\tSL-XBE_3_FC30CMAAAXX:5:20:1698:517\t0\t-\n+chr22\t51222602\t51222638\tSL-XBE_3_FC30CMAAAXX:5:24:103:330\t0\t+\n+chr22\t51222612\t51222648\tSL-XBE_3_FC30CMAAAXX:5:26:897:1871\t0\t-\n+chr22\t51222615\t51222651\tSL-XBE_3_FC30CMAAAXX:5:49:480:918\t0\t-\n+chr22\t51222615\t51222651\tSL-XBE_3_FC30CMAAAXX:5:54:425:1910\t0\t-\n+chr22\t51222669\t51222705\tSL-XBE_3_FC30CMAAAXX:5:79:277:1476\t0\t-\n+chr22\t51222673\t51222709\tSL-XBE_3_FC30CMAAAXX:5:84:1653:1979\t0\t+\n+chr22\t51222678\t51222714\tSL-XBE_3_FC30CMAAAXX:5:73:97:556\t0\t-\n+chr22\t51222700\t51222736\tSL-XBE_3_FC30CMAAAXX:5:9:1451:830\t25\t-\n+chr22\t51222711\t51222747\tSL-XBE_3_FC30CMAAAXX:5:89:721:351\t10\t-\n+chr22\t51222713\t51222749\tSL-XBE_3_FC30CMAAAXX:5:33:903:447\t24\t-\n+chr22\t51222743\t51222779\tSL-XBE_3_FC30CMAAAXX:5:68:89:20\t27\t-\n+chr22\t51222744\t51222780\tSL-XBE_3_FC30CMAAAXX:5:2:475:1162\t27\t-\n+chr22\t51222752\t51222788\tSL-XBE_3_FC30CMAAAXX:5:45:1449:1692\t18\t-\n+chr22\t51222763\t51222799\tSL-XBE_3_FC30CMAAAXX:5:94:797:1441\t0\t-\n+chr22\t51222784\t51222820\tSL-XBE_3_FC30CMAAAXX:5:95:111:366\t0\t-\n+chr22\t51222786\t51222822\tSL-XBE_3_FC30CMAAAXX:5:69:778:40\t0\t-\n+chr22\t51222789\t51222825\tSL-XBE_3_FC30CMAAAXX:5:22:1734:1139\t0\t-\n+chr22\t51222950\t51222986\tSL-XBE_3_FC30CMAAAXX:5:50:1673:646\t0\t-\n+chr22\t51223028\t51223064\tSL-XBE_3_FC30CMAAAXX:5:55:766:1690\t0\t-\n+chr22\t51223106\t51223142\tSL-XBE_3_FC30CMAAAXX:5:80:1352:909\t27\t-\n+chr22\t51224552\t51224588\tSL-XBE_3_FC30CMAAAXX:5:88:133:463\t0\t+\n+chr22\t51224724\t51224760\tSL-XBE_3_FC30CMAAAXX:5:80:852:479\t72\t-\n+chr22\t51228069\t51228105\tSL-XBE_3_FC30CMAAAXX:5:73:944:722\t0\t+\n+chr22\t51228538\t51228574\tSL-XBE_3_FC30CMAAAXX:5:48:506:379\t0\t-\n+chr22\t51229438\t51229474\tSL-XBE_3_FC30CMAAAXX:5:13:997:1058\t0\t+\n+chr22\t51234226\t51234262\tSL-XBE_3_FC30CMAAAXX:5:50:231:701\t0\t+\n+chr22\t51234579\t51234615\tSL-XBE_3_FC30CMAAAXX:5:55:1318:591\t18\t+\n+chr22\t51235800\t51235836\tSL-XBE_3_FC30CMAAAXX:5:5:271:853\t0\t+\n+chr22\t51241213\t51241249\tSL-XBE_3_FC30CMAAAXX:5:49:581:1477\t0\t-\n+chr22\t51242187\t51242223\tSL-XBE_3_FC30CMAAAXX:5:72:1761:1462\t0\t-\n' |
| b |
| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/K562H3k4me3Rep1_peaks.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/K562H3k4me3Rep1_peaks.xls Mon Jan 22 04:03:44 2018 -0500 |
| b |
| b'@@ -0,0 +1,650 @@\n+# This file is generated by MACS\n+chr\tstart\tend\tlength\tsummit\ttags\n+chr22\t16095745\t16097443\t1699\t551\t31\t85.59\t9.35\t10.58\n+chr22\t16097496\t16098978\t1483\t1033\t34\t73.20\t6.84\t17.95\n+chr22\t16190883\t16193697\t2815\t1802\t229\t1192.93\t25.68\t0.22\n+chr22\t16199803\t16202576\t2774\t1854\t94\t422.25\t14.58\t0.54\n+chr22\t16404139\t16404957\t819\t633\t16\t71.61\t10.06\t19.17\n+chr22\t16467078\t16468107\t1030\t455\t15\t64.74\t11.14\t27.33\n+chr22\t17079938\t17087399\t7462\t3936\t1082\t3100.00\t33.47\t0.63\n+chr22\t17198173\t17199825\t1653\t585\t50\t62.55\t5.65\t30.87\n+chr22\t17305354\t17306880\t1527\t776\t29\t56.44\t6.15\t44.93\n+chr22\t17504937\t17506060\t1124\t334\t25\t102.65\t8.75\t5.66\n+chr22\t17517105\t17520588\t3484\t1496\t202\t1144.62\t26.97\t0.21\n+chr22\t17564762\t17567248\t2487\t1273\t104\t549.76\t24.39\t0.41\n+chr22\t17639221\t17640779\t1559\t545\t71\t484.18\t27.95\t0.46\n+chr22\t17651479\t17653712\t2234\t881\t138\t929.89\t35.55\t0.25\n+chr22\t17847542\t17848819\t1278\t664\t21\t65.98\t7.66\t25.60\n+chr22\t17849020\t17850584\t1565\t1034\t35\t106.19\t10.94\t5.16\n+chr22\t18008491\t18009784\t1294\t427\t44\t251.39\t17.69\t1.04\n+chr22\t18110034\t18113200\t3167\t1282\t352\t2132.01\t36.31\t0.36\n+chr22\t18114915\t18117276\t2362\t1054\t69\t158.95\t8.20\t2.01\n+chr22\t18119731\t18123652\t3922\t1508\t518\t3100.00\t37.78\t0.63\n+chr22\t18155107\t18156464\t1358\t750\t27\t74.56\t6.73\t16.88\n+chr22\t18255474\t18258446\t2973\t987\t116\t542.80\t28.61\t0.40\n+chr22\t18259377\t18260980\t1604\t819\t37\t61.47\t6.02\t33.11\n+chr22\t18267629\t18270640\t3012\t2039\t77\t136.09\t9.84\t2.75\n+chr22\t18396326\t18398024\t1699\t535\t33\t53.77\t6.68\t54.32\n+chr22\t18398488\t18401633\t3146\t759\t129\t330.38\t9.62\t0.67\n+chr22\t18402174\t18404161\t1988\t888\t59\t140.91\t9.30\t2.51\n+chr22\t18462442\t18464468\t2027\t1243\t80\t429.05\t18.55\t0.54\n+chr22\t18482610\t18485387\t2778\t1802\t182\t1226.37\t36.46\t0.21\n+chr22\t18506171\t18507863\t1693\t964\t59\t216.30\t12.99\t1.25\n+chr22\t18558640\t18562948\t4309\t2364\t403\t2297.60\t39.47\t0.34\n+chr22\t18632202\t18633823\t1622\t755\t70\t307.34\t16.41\t0.73\n+chr22\t18754423\t18755296\t874\t363\t19\t66.31\t8.97\t25.19\n+chr22\t18820413\t18822075\t1663\t891\t47\t63.47\t6.25\t29.36\n+chr22\t18840835\t18842560\t1726\t874\t65\t58.27\t6.96\t39.83\n+chr22\t18890970\t18892794\t1825\t1041\t71\t328.87\t25.12\t0.67\n+chr22\t18892805\t18895391\t2587\t1330\t229\t1549.27\t32.94\t0.24\n+chr22\t19094933\t19099441\t4509\t2551\t242\t419.35\t12.24\t0.55\n+chr22\t19107267\t19111249\t3983\t1968\t519\t2945.30\t34.86\t0.53\n+chr22\t19130307\t19132984\t2678\t1680\t469\t2194.25\t25.00\t0.35\n+chr22\t19156318\t19162758\t6441\t3508\t1058\t3100.00\t32.29\t0.63\n+chr22\t19162800\t19167844\t5045\t4071\t540\t2032.79\t20.38\t0.33\n+chr22\t19188607\t19190674\t2068\t1177\t111\t263.12\t13.12\t0.94\n+chr22\t19246444\t19248471\t2028\t824\t110\t344.20\t12.11\t0.64\n+chr22\t19262401\t19264148\t1748\t1264\t59\t55.31\t4.77\t48.75\n+chr22\t19277778\t19280584\t2807\t1868\t480\t2971.61\t32.87\t0.55\n+chr22\t19383791\t19386211\t2421\t1259\t143\t189.90\t6.76\t1.49\n+chr22\t19406085\t19408091\t2007\t680\t98\t69.42\t4.19\t21.29\n+chr22\t19416109\t19421837\t5729\t4138\t1118\t3100.00\t49.28\t0.63\n+chr22\t19433432\t19436901\t3470\t1215\t553\t3100.00\t32.72\t0.63\n+chr22\t19464711\t19470616\t5906\t2380\t1245\t3100.00\t35.30\t0.63\n+chr22\t19553564\t19555149\t1586\t901\t42\t88.43\t7.58\t9.34\n+chr22\t19614151\t19616560\t2410\t1423\t155\t430.30\t11.85\t0.54\n+chr22\t19628206\t19629998\t1793\t753\t72\t99.23\t6.04\t6.29\n+chr22\t19630132\t19632979\t2848\t1642\t101\t69.38\t4.97\t21.32\n+chr22\t19650970\t19653665\t2696\t868\t60\t63.15\t4.48\t29.92\n+chr22\t19678284\t19680168\t1885\t1116\t149\t246.40\t10.60\t1.06\n+chr22\t19700699\t19703180\t2482\t1872\t138\t470.21\t18.37\t0.50\n+chr22\t19704678\t19709721\t5044\t1475\t375\t1410.03\t20.06\t0.23\n+chr22\t19709810\t19713364\t3555\t1451\t340\t1626.62\t23.48\t0.26\n+chr22\t19717590\t19719520\t1931\t912\t130\t440.12\t19.82\t0.54\n+chr22\t19743543\t19745398\t1856\t508\t81\t209.67\t10.53\t1.32\n+chr22\t19747026\t19748594\t1569\t905\t36\t61.70\t8.58\t32.58\n+chr22\t19748602\t19751068\t2467\t738\t179\t851.47\t14.27\t0.29\n+chr22\t19753733\t19755707\t1975\t884\t60\t139.39\t8.62\t2.57\n+chr22\t19759230\t19763015\t3786\t1290\t150\t226.42\t8.69\t1.19\n+chr22\t19767002\t19768787\t1786\t922\t93\t91.85\t6.14\t8.27\n+chr22\t19793330\t19795127\t1798\t894\t47\t50.56\t6.41\t67.56\n+chr22\t19801518\t19804153\t2636\t1501\t88\t61.68\t6.25\t32.64\n+chr22\t19813157\t19816195\t3039\t2239\t141\t173.01\t7.53\t1.78\n+chr2'..b'\t12.40\t1.38\n+chr22\t46644955\t46645585\t631\t333\t13\t73.34\t10.63\t17.87\n+chr22\t46645655\t46648875\t3221\t1043\t176\t1390.23\t40.87\t0.22\n+chr22\t46663103\t46665621\t2519\t1193\t120\t885.53\t38.57\t0.28\n+chr22\t46691392\t46694232\t2841\t1083\t143\t847.13\t26.43\t0.29\n+chr22\t46730646\t46733240\t2595\t1784\t150\t878.29\t17.97\t0.28\n+chr22\t46786198\t46787218\t1021\t556\t18\t87.84\t17.50\t9.61\n+chr22\t46851230\t46852461\t1232\t777\t23\t73.52\t7.95\t17.78\n+chr22\t46959098\t46960261\t1164\t566\t24\t126.34\t19.09\t3.26\n+chr22\t46971851\t46972747\t897\t434\t13\t50.37\t9.57\t68.65\n+chr22\t46973058\t46976616\t3559\t865\t137\t958.64\t31.82\t0.22\n+chr22\t46999309\t47001409\t2101\t653\t61\t309.99\t18.14\t0.72\n+chr22\t47044982\t47046222\t1241\t699\t23\t72.95\t11.93\t18.07\n+chr22\t47047805\t47048545\t741\t152\t11\t52.02\t11.14\t61.00\n+chr22\t47132700\t47135177\t2478\t793\t57\t299.93\t17.50\t0.76\n+chr22\t47149605\t47151076\t1472\t715\t37\t213.97\t19.09\t1.26\n+chr22\t47156427\t47160194\t3768\t1641\t256\t2225.14\t54.69\t0.31\n+chr22\t47330272\t47332573\t2302\t1362\t63\t178.04\t8.89\t1.68\n+chr22\t47485316\t47488195\t2880\t1083\t116\t672.89\t20.78\t0.31\n+chr22\t47732688\t47733415\t728\t541\t11\t52.78\t11.14\t58.04\n+chr22\t48026267\t48029425\t3159\t1483\t240\t2081.74\t60.76\t0.34\n+chr22\t48074275\t48075002\t728\t532\t15\t76.53\t11.14\t15.57\n+chr22\t49447787\t49448819\t1033\t651\t15\t64.58\t11.14\t27.54\n+chr22\t49764635\t49765621\t987\t465\t30\t167.53\t19.44\t1.88\n+chr22\t50048953\t50052069\t3117\t1968\t194\t1371.23\t33.81\t0.22\n+chr22\t50097692\t50098812\t1121\t398\t20\t62.58\t8.95\t30.83\n+chr22\t50117561\t50119066\t1506\t892\t25\t85.89\t8.51\t10.46\n+chr22\t50179678\t50180601\t924\t294\t18\t69.29\t10.94\t21.45\n+chr22\t50200909\t50202776\t1868\t1122\t58\t368.77\t20.31\t0.61\n+chr22\t50219320\t50221212\t1893\t691\t68\t473.44\t28.64\t0.51\n+chr22\t50246390\t50249788\t3399\t1956\t119\t655.03\t29.17\t0.32\n+chr22\t50310391\t50313542\t3152\t1305\t118\t650.70\t25.16\t0.32\n+chr22\t50328011\t50328960\t950\t555\t18\t92.87\t11.14\t7.94\n+chr22\t50329728\t50330587\t860\t440\t12\t52.64\t11.14\t58.65\n+chr22\t50352391\t50357284\t4894\t3273\t204\t1497.61\t36.60\t0.23\n+chr22\t50437292\t50439071\t1780\t535\t41\t221.14\t27.05\t1.23\n+chr22\t50523560\t50524565\t1006\t327\t17\t71.28\t9.57\t19.45\n+chr22\t50543552\t50544765\t1214\t680\t24\t51.47\t9.48\t63.16\n+chr22\t50555334\t50558338\t3005\t634\t86\t336.90\t15.96\t0.65\n+chr22\t50606763\t50608437\t1675\t293\t27\t58.50\t6.38\t39.33\n+chr22\t50608791\t50609989\t1199\t527\t22\t107.25\t17.50\t4.98\n+chr22\t50624344\t50626062\t1719\t982\t58\t381.89\t23.87\t0.62\n+chr22\t50628254\t50629940\t1687\t892\t57\t386.19\t39.78\t0.61\n+chr22\t50638189\t50641455\t3267\t2181\t122\t840.24\t30.23\t0.29\n+chr22\t50679295\t50680533\t1239\t605\t23\t112.43\t17.50\t4.42\n+chr22\t50680542\t50681923\t1382\t873\t53\t262.31\t15.49\t0.94\n+chr22\t50682037\t50684770\t2734\t1171\t223\t1892.01\t42.66\t0.31\n+chr22\t50688417\t50690159\t1743\t1030\t56\t358.28\t33.41\t0.61\n+chr22\t50698168\t50702116\t3949\t1226\t109\t632.27\t28.64\t0.34\n+chr22\t50707546\t50708451\t906\t727\t16\t79.89\t12.73\t13.51\n+chr22\t50708578\t50710245\t1668\t642\t44\t249.91\t20.69\t1.05\n+chr22\t50744154\t50746561\t2408\t1380\t63\t360.86\t27.05\t0.62\n+chr22\t50752385\t50753651\t1267\t824\t27\t110.78\t12.70\t4.60\n+chr22\t50756814\t50758035\t1222\t795\t23\t113.65\t14.32\t4.27\n+chr22\t50764343\t50767132\t2790\t826\t91\t388.78\t17.32\t0.60\n+chr22\t50768593\t50770366\t1774\t746\t100\t870.04\t46.14\t0.28\n+chr22\t50780130\t50782495\t2366\t1404\t94\t684.37\t28.64\t0.31\n+chr22\t50911725\t50913482\t1758\t845\t52\t322.67\t28.12\t0.67\n+chr22\t50913544\t50914308\t765\t189\t25\t166.70\t23.87\t1.88\n+chr22\t50919355\t50921489\t2135\t1094\t59\t351.84\t19.09\t0.62\n+chr22\t50936245\t50937827\t1583\t1085\t52\t252.70\t15.91\t1.04\n+chr22\t50944937\t50946179\t1243\t615\t94\t934.78\t44.55\t0.25\n+chr22\t50946617\t50948871\t2255\t602\t132\t851.83\t25.52\t0.30\n+chr22\t50962507\t50966139\t3633\t1417\t138\t928.32\t26.60\t0.25\n+chr22\t50977507\t50978750\t1244\t386\t27\t89.79\t7.29\t8.91\n+chr22\t51001055\t51002326\t1272\t539\t89\t857.32\t57.28\t0.30\n+chr22\t51020032\t51022705\t2674\t1071\t115\t869.15\t44.55\t0.28\n+chr22\t51051823\t51052907\t1085\t310\t19\t90.05\t14.06\t8.84\n+chr22\t51059873\t51061094\t1222\t486\t28\t106.49\t10.94\t5.13\n+chr22\t51065592\t51067592\t2001\t1543\t126\t1110.64\t42.53\t0.20\n+chr22\t51180653\t51181336\t684\t514\t11\t55.49\t12.73\t48.18\n+chr22\t51195232\t51196467\t1236\t550\t21\t96.94\t14.32\t6.78\n+chr22\t51220807\t51223293\t2487\t1018\t141\t950.30\t29.83\t0.23\n' |
| b |
| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/K562H3k4me3Rep1_reads.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/K562H3k4me3Rep1_reads.bed Mon Jan 22 04:03:44 2018 -0500 |
| b |
| b'@@ -0,0 +1,205035 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|
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| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/output_dir/output_figures/sample1_vs_sample2_MA_plot_after_normalization.png |
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| Binary file test-data/output_dir/output_figures/sample1_vs_sample2_MA_plot_after_normalization.png has changed |
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| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/output_dir/output_figures/sample1_vs_sample2_MA_plot_before_normalization.png |
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| Binary file test-data/output_dir/output_figures/sample1_vs_sample2_MA_plot_before_normalization.png has changed |
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| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/output_dir/output_figures/sample1_vs_sample2_MA_plot_with_P-value.png |
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| Binary file test-data/output_dir/output_figures/sample1_vs_sample2_MA_plot_with_P-value.png has changed |
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| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/output_dir/output_figures/sample1_vs_sample2_read_density_on_common_peaks.png |
| b |
| Binary file test-data/output_dir/output_figures/sample1_vs_sample2_read_density_on_common_peaks.png has changed |
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| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/output_dir/output_filters/sample1_M_above_1.0_biased_peaks.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dir/output_filters/sample1_M_above_1.0_biased_peaks.bed Mon Jan 22 04:03:44 2018 -0500 |
| b |
| b'@@ -0,0 +1,194 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|
| b |
| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/output_dir/output_filters/sample1_M_below_-1.0_biased_peaks.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dir/output_filters/sample1_M_below_-1.0_biased_peaks.bed Mon Jan 22 04:03:44 2018 -0500 |
| b |
| b'@@ -0,0 +1,323 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|
| b |
| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/output_dir/output_filters/sample1_vs_sample2_unbiased_peaks.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dir/output_filters/sample1_vs_sample2_unbiased_peaks.bed Mon Jan 22 04:03:44 2018 -0500 |
| b |
| b'@@ -0,0 +1,254 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|
| b |
| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/output_dir/output_tracks/sample1_vs_sample2_A_values.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dir/output_tracks/sample1_vs_sample2_A_values.wig Mon Jan 22 04:03:44 2018 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/output_dir/output_tracks/sample1_vs_sample2_M_values.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dir/output_tracks/sample1_vs_sample2_M_values.wig Mon Jan 22 04:03:44 2018 -0500 |
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| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/output_dir/output_tracks/sample1_vs_sample2_P_values.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dir/output_tracks/sample1_vs_sample2_P_values.wig Mon Jan 22 04:03:44 2018 -0500 |
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|
| b |
| diff -r 000000000000 -r 9cd4a30cb4f8 test-data/output_dir/sample1_vs_sample2_all_MAvalues.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dir/sample1_vs_sample2_all_MAvalues.xls Mon Jan 22 04:03:44 2018 -0500 |
| b |
| b'@@ -0,0 +1,847 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|
