Bowtie2: gtf file - annotation file

Question

[KVC_bioinfo]

I am trying to create index files using bowtie2 for the human genome. I was wondering if I can use the annotation file while creating indexes. I read in manual I could not find such option. Am I missing something?

Answer 1

[Sej Modha]

I don't think bowtie2 supports gtf format, however, a splice aware aligner such as tophat2 uses bowtie2 to align reads to the genome. However, tophat2 is out of development and replaced by HISAT2.

Answer 2

[Devon Ryan]

No, you can't do that since bowtie2 has no conception of what a splice site is. As Sej Modha wrote, you're looking for STAR or hisat2.