RNAseq alignements
I am comparing the alignments with HISAT vs tophat in mouse genome. I have around 30 million SE illumina next seq data and aligned with HISAT and Tophat using default settings. I found the number of alignments are much more (around 30% more) in TopHat as compared to HISAT. I was expecting HISAT shoudl have more alignment than TopHat. Has any one else on this forum observed such pattern. any possible reason?
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I think the first thing anyone is going to ask for are the command lines used.
I'd be interested in the results of aligning with BBMap... for vertebrate RNA, just add the flag "maxindel=400k".
Personally, I don't think that TopHat (or tuxedo in general) is a useful platform.