Question: Bowtie2: gtf file - annotation file
0
gravatar for KVC_bioinfo
3.1 years ago by
KVC_bioinfo510
Boston
KVC_bioinfo510 wrote:

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?

aligner bowtie2 gtf • 2.0k views
ADD COMMENTlink modified 3.1 years ago by Devon Ryan97k • written 3.1 years ago by KVC_bioinfo510
2
gravatar for Sej Modha
3.1 years ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

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.

ADD COMMENTlink written 3.1 years ago by Sej Modha4.7k
1
gravatar for Devon Ryan
3.1 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

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.

ADD COMMENTlink written 3.1 years ago by Devon Ryan97k
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