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Junctions.bed file in hisat2?

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  • 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

  • #2
    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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