Mercurial > repos > saharlcc > isoem2_isode2
changeset 11:630d5a01ef13 draft
Minor change in IsoDE2 interface
| author | saharlcc |
|---|---|
| date | Fri, 17 Mar 2017 06:47:46 -0400 |
| parents | 78d03bf22a1f |
| children | be08c88b353e |
| files | isoem2_isode2/isoDE.xml isoem2_isode2/isoDE2.sh |
| diffstat | 2 files changed, 13 insertions(+), 14 deletions(-) [+] |
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--- a/isoem2_isode2/isoDE.xml Thu Mar 16 13:44:03 2017 -0400 +++ b/isoem2_isode2/isoDE.xml Fri Mar 17 06:47:46 2017 -0400 @@ -36,7 +36,7 @@ </repeat> - <param name="pval" label="p-value" type="float" value="0.05" help="Desired p-value to for which a reliable fold change level will be reported" /> + <param name="pval" label="Significance level" type="float" value="0.05" help="Desired significance level for which a conservative (reliable) fold change will be reported" /> </inputs> <outputs> @@ -50,13 +50,12 @@ **What it does** Computes gene and isoform differential expression between two conditions (example tumor and normal) for both Fragment per Kilobase of transcript length per Million -bases (FPKM) and Transcripts per Million (TPM) values. The computation is based on the boostraping output generated by IsoEM2. The number of bootstrap iterations for -IsoEM2 should be >= 20 (suggested 200). +bases (FPKM) and Transcripts per Million (TPM) values. The computation is based on the boostraping output generated by IsoEM2. **Input** * - One or more IsoEM output files (compressed tar files) for each of the two conditions. More than one file can be used if there are replicated for either condition -* - Desired p-value to for which a reliable fold change level will be reported +* - Desired Significance level for which a reliable fold change level will be reported * @@ -66,14 +65,14 @@ * four output files containinag results for Gene FPKM DE, Gene TPM DE, Isoform FPKM DE, and Isoform TPM DE. The four files have identical format with the following fields * 1- Gene/isoform ID -* 2- Reliable log_2(FC) : conservative estimate of fold change in log base 2. -* For the confidence level specified by the input p-value, fold change of gene/isoform abundance (FPKM/TPM) in condition 2 compared condition 1 is +* 2- Conservative log_2(FC) : conservative estimate of fold change in log base 2. +* For the confidence level as input, fold change of gene/isoform abundance (FPKM/TPM) in condition 2 compared condition 1 is * at least 2 ^ absoulte value of this field.The sign indicates the direction, +ve means over expressed in condition 2, -ve means underexpressed in * condition 1. 0 indicates that no change was detected. -* 3- log_2(condition 2 FPKM (or TPM)/condition 1 FPKM(or TPM)) based on IsoEM2 run without bootstrapping -* 4- condition 1 FPKM (or TPM) based on IsoEM2 run without bootstrapping -* 5- condition 2 FPKM (or TPM) based on IsoEM2 run without bootstrapping - +* 3- log_2(condition 2 FPKM (or TPM)/condition 1 FPKM(or TPM)) based on IsoEM2 run without bootstrapping (average FPKM or TPM if replicates used) +* 4- condition 1 FPKM (or TPM) based on IsoEM2 run without bootstrapping (average if replicates used) +* 5- condition 2 FPKM (or TPM) based on IsoEM2 run without bootstrapping (average if replicates used) + </help> </tool>
--- a/isoem2_isode2/isoDE2.sh Thu Mar 16 13:44:03 2017 -0400 +++ b/isoem2_isode2/isoDE2.sh Fri Mar 17 06:47:46 2017 -0400 @@ -141,7 +141,7 @@ date -awk '{if (NR == 1) {print "Gene ID\tConfident log2 FC\t Single run log2 FC\t c1 FPKM\tc2 FPKM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t" $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${geneFPKMout_file} +awk '{if (NR == 1) {print "Gene ID\tConservative log2 FC\t Single run log2 FC\t c1 average FPKM\tc2 average FPKM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t" $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${geneFPKMout_file} cd .. @@ -164,7 +164,7 @@ echo awk command date pwd -awk '{if (NR == 1) {print "Isoform ID\tConfident log2 FC\t Single run log2 FC\t c1 FPKM\tc2 FPKM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t" $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${isoFPKMout_file} +awk '{if (NR == 1) {print "Isoform ID\tConservative log2 FC\t Single run log2 FC\t c1 average FPKM\tc2 average FPKM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t" $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${isoFPKMout_file} cd .. @@ -184,7 +184,7 @@ echo awk command date pwd -awk '{if (NR == 1) {print "Gene ID\tConfident log2 FC\t Single run log2 FC\t c1 TPM\tc2 TPM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t" $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${geneTPMout_file} +awk '{if (NR == 1) {print "Gene ID\tConservative log2 FC\t Single run log2 FC\t c1 average TPM\tc2 average TPM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t" $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${geneTPMout_file} cd .. @@ -204,7 +204,7 @@ echo awk command date -awk '{if (NR == 1) {print "Isoform ID\tConfident log2 FC\t Single run log2 FC\t c1 TPM\tc2 TPM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t" $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${isoTPMout_file} +awk '{if (NR == 1) {print "Conservative Isoform ID\tConfident log2 FC\t Single run log2 FC\t c1 average TPM\tc2 average TPM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t" $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${isoTPMout_file} cd ..