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Old 12-18-2012, 02:05 AM   #1
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Location: Munich

Join Date: Oct 2012
Posts: 6
Default bowtie2 vs. Tophat2 RNA-Seq


I have PE 100 Drosophila HiSeq RNA-Seq data. I mapped the same data using Tophat2 (changed only the inner distance estimated by Cufflinks) and Bowtie2 against the genome.

I converted the SAM file to Bedgraph file using HTSeq.

Somehow in the case Tophat2 I see "flat" intronic coverage and in bowtie2 not (see attachment). Did anyone have similar issues?

The read counts per gene in the exons obtained by htseq-count do not really differ. Only in a few special cases.


Attached Images
File Type: png chrX-3984847-4143770.png (15.6 KB, 24 views)
File Type: png chr3L-6121863-6127664.png (14.3 KB, 12 views)
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