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:
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):
why do i get this error:
what could be the problem?
thank you in advance...
dietmar
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
____________________________________________________________
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
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]
thank you in advance...
dietmar