Hi,
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.
Thanks,
T.
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.
Thanks,
T.
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