[danwiththeplan]

the funny part in all of this is that Tophat bothered me enough for me to stop using it a couple years ago so my best solution is to use something else but OP seems pretty committed to it. I checked back in the thread and OP mentioned gsnap in post #12 so maybe I missed if that was redacted at some point.

Yes, seems to be a bit of confusion as to whether GSNAP (post 12) or SNAP (post 21) is producing 46% alignment rate, OP has contradictory posts.

[Studentlost]

Sorry the SNAP in post 21 was a typo, I meant GSNAP. I haven't run it on GSNAP yet. I used Bowtie2 when I got the 46% alignment.

I am getting my alignment information via the align_summary.txt file.

[sdriscoll]

Let us know when you try some of the suggestions we've posted otherwise we will get nowhere. Thanks.

[Studentlost]

I'm going to align with Star and I'll dump the alignment information for Bowtie2, Tophat2, and Star on here once that's finished this weekend so you guys can give me some insight.

Thanks again for all your help.

[bbm]

any update from the OP? I'm have similar problem...