Thread: subread
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Old 12-04-2011, 10:40 AM   #1
hanshart
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Location: Germany

Join Date: Nov 2011
Posts: 27
Default subread: "a superfast read aligner"

Hello

Has anyone of you allready tried subread ("subread: a superfast read aligner": http://sourceforge.net/projects/subread/)?
I'm very new to RNA-Seq. I'm examining Illumina HiSeq data for different tissues of the human body. At first I used bowtie2 (beta3, without splicing library) and it mapped about 85% of the reads to the hg19 genome (which is quite good I think?!) using the standard parameters for bowtie2 end-to-end alignment.
After that I tried out subread with standard settings. Subread should be able to detect splicing events. It actually mapped 95 to 98% of my reads to hg19 in the same time as bowtie2 did!
I'm asking if anybody is experienced with subread and could say something about the quality of the program/mapping process and traps or drawbacks of it? I'm wondering why it is not mentioned anywhere although it seems to be very fast and powerful?
Thank you.

Last edited by hanshart; 12-04-2011 at 02:18 PM.
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