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Bowtie2: gtf file - annotation file

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?

bowtie2 gtf aligner
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updated by Devon Ryan Devon Ryan • written by KVC_bioinfo KVC_bioinfo

2 answers

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.

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written by Sej Modha Sej Modha

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.

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written by Devon Ryan Devon Ryan

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