Originally posted by sdriscoll
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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. -
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.Comment
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Let us know when you try some of the suggestions we've posted otherwise we will get nowhere. Thanks./* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */Comment
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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.Comment
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any update from the OP? I'm have similar problem...Comment
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