I have been using htseq-count with great success, except for one particular type of genome feature, the transposable elements (te).
There is no attribute defined in the gff file, and this appears to always be the case for this type of genome feature.
I am not involved in upstream sequencing activities, and do not understand why attributes are not always available. I do not entirely understand why htseq-count needs to know the attribute of interest, unless it must choose between multiple attributes.
Here are the first few lines of my te.gff file:
Below, the command I hopelessly attempted to execute:
/usr/bin/python -m HTSeq.scripts.count --format=bam --stranded=no --type=Tandem_Repeat --idattr=. --mode=union ./BAM/ovo1.bam ./features/te.gff > ovo1te.counts
Error occured when processing GFF file (line 1 of file ./features/te.gff):
Failure parsing GFF attribute line
[Exception type: ValueError, raised in __init__.py:164]
Can someone please explain why htseq-count needs to know the attribute? Is there a way to run it with no attribute defined?
Kind Regards, Elizabeth
There is no attribute defined in the gff file, and this appears to always be the case for this type of genome feature.
I am not involved in upstream sequencing activities, and do not understand why attributes are not always available. I do not entirely understand why htseq-count needs to know the attribute of interest, unless it must choose between multiple attributes.
Here are the first few lines of my te.gff file:
Code:
C21242 TRF Tandem_Repeat 38 100 72 + . . C21306 TRF Tandem_Repeat 35 143 112 + . . C21306 TRF Tandem_Repeat 574 947 208 + . .
/usr/bin/python -m HTSeq.scripts.count --format=bam --stranded=no --type=Tandem_Repeat --idattr=. --mode=union ./BAM/ovo1.bam ./features/te.gff > ovo1te.counts
Error occured when processing GFF file (line 1 of file ./features/te.gff):
Failure parsing GFF attribute line
[Exception type: ValueError, raised in __init__.py:164]
Can someone please explain why htseq-count needs to know the attribute? Is there a way to run it with no attribute defined?
Kind Regards, Elizabeth
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