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Old 02-18-2013, 12:39 AM   #2
pettervikman
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Location: Sweden

Join Date: Nov 2009
Posts: 23
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I've also noticed that tophat (v.2.0.7) is extremly slow when run in conjunction with bowtie2. I was going to have a look at my options ( -r 100 -m 1 -p 1 --coverage-search --microexon-search --library-type fr-unstranded) to see if there were anything there. According to the program the coverage search can be really slow but I've also found that the alignments per se is really slow. I multiplex several samples rather then having many cores on one samples so it takes more then one week per sample (human RNA, around 40-50 million reads).

We have started looking into star which is way (more then factor 10) faster. But since we haven't evaluated that just yet I'd really like to keep on using tophat.

/Petter
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