bowtie2 vs. Tophat2 RNA-Seq

[tschauer]

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.

[rboettcher]

TopHat2 is designed for RNAseq and therefore splicing aware, whereas bowtie2 is designed for DNAseq and therefore cannot handle splice junctions.

Since your RNAseq is expected to come from exons only, bowtie2 maps to the exonic regions while TopHat2 considers the introns in between as spanned by split reads or read pairs. Therefore I assume your bedgraph visualizes the spanning reads by inserting these "flat" regions in between your exons.

[tschauer]

Thanks for the quick reply.

I also assumed so that these are only the "connections". In that case these graphs have to be read somewhat differently...