chocotwig
chocotwig
I use bowtie2 to index, `bowtie2-build $sourceDir/$sourceName $descriptor` Then I use TopHat v2.0.13 `tophat --read-mismatches 4 --read-gap-length 5 --segment-mismatches 3 --read-edit-dist 5 $workDir/$descriptor read_pair1 read_pair2` And yes, there seem to...
Hi, Thanks, the output for the command you suggested is ```2157287``` What are your thoughts on this? I will also try Hisat in the meanwhile. Thanks!
Okay! Thanks - could you explain what you mean by local hits? Hits for individual reads one at a time, as opposed to the entire genome dataset altogether? Thanks!