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Old 03-06-2017, 02:00 PM   #1
badribioinfo
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Default 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
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Old 03-12-2017, 09:47 AM   #2
badribioinfo
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Location: USA

Join Date: Dec 2016
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Quote:
Originally Posted by badribioinfo View Post
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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hisat2, pipeline development, splicing, splicing annotation

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