Question: Tophat and Bowtie2
gravatar for anitha.b
9 months ago by
anitha.b0 wrote:


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

rna-seq sequence alignment • 295 views
ADD COMMENTlink modified 9 months ago by Chirag Parsania430 • written 9 months ago by anitha.b0

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 ?

ADD REPLYlink written 9 months ago by Santosh Anand3.4k
gravatar for Chirag Parsania
9 months ago by
University of Macau
Chirag Parsania430 wrote:

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.

ADD COMMENTlink written 9 months ago by Chirag Parsania430
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