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Old 04-10-2013, 02:26 PM   #1
Julien Roux
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Location: Chicago

Join Date: Dec 2011
Posts: 24
Default Tophat: generate junctions.bed file from BAM file

Dear all,
I have previously mapped RNA-seq samples to the human genome using Tophat 2.0.6. This generated an "accepted_hits.bam" result file, and a "junctions.bed" file I am interested in for details on exon-exon junctions mapping.
To be sure to compare fairly my different samples, I want to downsample the BAM files to have the same number of mapped reads for each sample. This is pretty straighforward using samtools or picard.
Now I would like to regenerate new "junctions.bed" files from the downsampled BAM files. I couldn't find in the log files which program of the tophat package does that.
Anyone ever dealt with a similar issue? Any hint?
Thanks for your help
Julien
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