Hi,
I have run htseq like this:
htseq-count sorted.bam my.gff -i ID
and my GFF entries are in this format:
chr1 . . 58812138 58812884 . + . ID="something";
but at the end all reads fall into the no_feature?! So probably I miss something?
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written
by
manekineko
You need a feature type column (3rd column). Usually it's transcript/exon or something like that. Just name it whatever you want and specify the name with the -t flag.
So let's say you have:
chr1 . myFeature 58812138 58812884 . + . ID="something";
Run it with:
htseq-count sorted.bam my.gff -i ID -t myFeature
Should it be unique or the 3rd column can be all the same and ID is unique? So I should keep the -i flag and use also -t flag?
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written
by
manekineko
3rd column should all be the same. It's just a feature type so htseq-count would know what features to count for. ID should be unique. You can use both -i and -t together.
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written
by
Damian Kao
Do you know why is working with a SAM that is 2G but when I run with larger SAM 16GM it gives me error:
53 GFF lines processed.
Error occured when reading beginning of SAM/BAM file.
[Exception type: StopIteration, raised in count.py:84]
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