Junctions.bed file in hisat2?

badribioinfo · 03-06-2017, 03:00 PM

Hi,
I was wondering if there is a way I can generate junctions.bed file from hisat2 just like the one in tophat.

Hisat2 documentation says use extract_splice_site.py python script but that gets splice site from gtf file, is there a way to know splice sites and no of reads associated with those sites using hisat2?

Thanks

badribioinfo · 03-12-2017, 10:47 AM

Quote:

Originally Posted by badribioinfo

Hi,
I was wondering if there is a way I can generate junctions.bed file from hisat2 just like the one in tophat.

Hisat2 documentation says use extract_splice_site.py python script but that gets splice site from gtf file, is there a way to know splice sites and no of reads associated with those sites using hisat2?

Thanks

Anyhelp is appreciated!

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03-06-2017, 03:00 PM	#1
badribioinfo Junior Member Location: USA Join Date: Dec 2016 Posts: 2	Junctions.bed file in hisat2? Hi, I was wondering if there is a way I can generate junctions.bed file from hisat2 just like the one in tophat. Hisat2 documentation says use extract_splice_site.py python script but that gets splice site from gtf file, is there a way to know splice sites and no of reads associated with those sites using hisat2? Thanks