Mercurial > repos > siyuan > prada
view pyPRADA_1.2/testdata/readme.txt @ 1:03815b87eb65 draft
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author | siyuan |
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date | Fri, 21 Feb 2014 18:08:37 -0500 |
parents | acc2ca1a3ba4 |
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TEST EXAMPLES To run these examples, set your PBS queue to short, walltime to 1:00:00 and ppn to 2 For the following exmaples, I assume the current location is the PRADA directory Please use "tar xzvf U87_chr17p13.2.end1.fastq.tar.gz" to unzip the fastq file. Please see manual how to add PRADA to system path. 1. Run PRADA from BAM ./prada-preprocess-bi -inputdir testdata -sample U87_chr17p13.2 -tag U87 -step 1_1 -pbs frombam -outdir testdata/test1 -submit yes 2. Run PRADA from FASTQ ./prada-preprocess-bi -inputdir testdata -sample U87_chr17p13.2 -tag U87 -step 2_e1_1 -pbs fromfq -outdir testdata/test2 -submit yes 3. Run Fusion Module ./prada-fusion -bam testdata/test1/U87_chr17p13.2.withRG.GATKRecalibrated.flagged.bam -junL 50 -outdir testdata/fusion 4. Run frame prediction ./prada-frame -conf conf.txt -i testdata/frame_test.txt -docstr frame_test_result -outdir testdata/ 5. Run homology prediction ./prada-homology -i testdata/homology_test.txt -o testdata/homology_test_result.txt -tmpdir testdata/tmp 6. Run GUESS-ft ./prada-guess-ft SPAG7 CAMTA2 -inputbam testdata/test1/U87_chr17p13.2.withRG.GATKRecalibrated.flagged.bam -junL 50 -outdir testdata/SPAG7_CAMTA2