Hello.
I am working on two RNA seq data from different conditions.
Now I am using tophat - cufflinks pipe line.
At first time, I ran tophat seperately each sam files (previous version Tophat was used).
Yesterday, I learned that two sample can be pooled in tophat process and ran tophat(v 1.1.0) as below.
$ tophat /rnaseq/bowtie/indexes/hg19 s_1_sequence.txt,s_2_sequence.txt
After run, I found that only one Bam file (accepted_hits.bam).
Because two RNA-seq data was processed, I guess that Tophat might report to Bam files.
Does it mean that I misunderstood something?
Or is it possible to split up again as quote below?
I am working on two RNA seq data from different conditions.
Now I am using tophat - cufflinks pipe line.
At first time, I ran tophat seperately each sam files (previous version Tophat was used).
Yesterday, I learned that two sample can be pooled in tophat process and ran tophat(v 1.1.0) as below.
$ tophat /rnaseq/bowtie/indexes/hg19 s_1_sequence.txt,s_2_sequence.txt
After run, I found that only one Bam file (accepted_hits.bam).
Because two RNA-seq data was processed, I guess that Tophat might report to Bam files.
Does it mean that I misunderstood something?
Or is it possible to split up again as quote below?
If you do pool the reads, you could also rename them to tag them by sample, so you can split the sample alignments up again after the TopHat run if needed.
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