Not sure how many people have tried this new version. I'm a big fan of the transcriptome alignment phase this new version includes (ie. Align to transcritopme, then genome, then split remaining reads to attempt alignment to genome) as most mRNAseq reads (60+ percent) will align to known transcriptome references using bwa or your favorite aligner in a very short amount of time. So that is the good news...
The bad news, at least on my first test run, the sample I tested had 71% alignment using Tophat v1.3.2 and now with the new version, which I expected to increase the percent alignment it dropped to 62%. Oddly the 62% is almost exactly the alignment frequency (63%) I see when I align to transcriptome reference using bwa. Has anyone else noted this odd behavior or percent aligned decreasing with this version?
The bad news, at least on my first test run, the sample I tested had 71% alignment using Tophat v1.3.2 and now with the new version, which I expected to increase the percent alignment it dropped to 62%. Oddly the 62% is almost exactly the alignment frequency (63%) I see when I align to transcriptome reference using bwa. Has anyone else noted this odd behavior or percent aligned decreasing with this version?
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