Tophat and Bowtie2

Question

[anitha.b]

Hi,

One of my sequnce data is aligned with tophat, alignment rate is 6%. If the same sequence is aligned with bowtie2 means, alignment rate is 96%. why i am getting less alignment rate in tophat compared to bowtie2? Any suggestions please.

Thanks, Anitha

[Santosh Anand]

Is your data RNA-seq? I find it intriguing that you first tried Tophat (a splice aware aligner) and then Bowtie2 and then that the alignment rate with Bowtie2 is so high. Did you check that the Bowtie version, which TopHat is using, is the same as the one you used for 96% alignment ?

Answer 1

[Chirag Parsania]

I dont know the reason why tophat is giving so less alignment. I would expact more aligned reads with tophat compare to bowtie. I would suggest you to use HISAT which new and alternative to tophat , developed by same group and they also recommend to use it over tophat.