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  • HTseq count problem

    hello,

    i have a sorted sam file from stampy (paired end) mapped against all viral sequences (multiFA-file) looking like this:
    _____________________________
    >AC_000001.1
    CATCATCAATAATAT...
    >AC_000002.1
    CATCATCAATAATCT...
    ...
    _____________________________

    stampy command:
    Code:
    $stampy/stampy.py --substitutionrate=0.01 -t 20 --sensitive --xcigar -g $index/viruses -h $index/viruses -o out.sam \
    	-M $fq1 $fq2
    and made an own gtf file from this information like this:
    ____________________________________________________________
    AC_000001.1 virus genome 1 33034 . . . gene_id "AC_000001.1";
    AC_000002.1 virus genome 1 34446 . . . gene_id "AC_000002.1";
    AC_000003.1 virus genome 1 30536 . . . gene_id "AC_000003.1";
    ____________________________________________________________


    now I want count all mapped read-pairs, which map both to one virus genome (i.e. multiFA-entry):

    Code:
    htseq-count -m union -s no -t genome -i gene_id $sam $gff > ${name}.count
    why do i get this error:
    Code:
    Error occured in line 1 of file /home/ws/Data/Oncotest/fa/viral_genome_sorted.fa/viral_genome.GFF.
    Error: [Errno 20] Not a directory: '/home/ws/Data/Oncotest/fa/viral_genome_sorted.fa/viral_genome.GFF'
    [Exception type: IOError, raised in __init__.py:45]
    what could be the problem?

    thank you in advance...

    dietmar

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