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Old 12-02-2015, 03:34 PM   #1
pshah
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Location: San Francisco

Join Date: Sep 2015
Posts: 3
Default htseq-count failure parsing GFF attribute line

Hi,
I am trying to generate a read counts file for my ChIP-seq data using htseq-count. Here is what I have done so far:

1. Call ChIP-seq peaks and output BED file in MACS2
2. Convert BED to GFF in Galaxy
2. Run htseq-count with the following command and error:

Code:
-bash-4.1$ htseq-count -f bam -s no -t feature M1-cbx5_sorted.bam Rep1_cbx5_merge.gff
Error occured when processing GFF file (line 1 of file Rep1_cbx5_merge.gff):
  Failure parsing GFF attribute line
  [Exception type: ValueError, raised in __init__.py:164]
I suspect that there is something wrong with my GFF input, but I am not sure what.

Here is what my GFF file looks like:
Code:
-bash-4.1$ head Rep1_cbx5_merge_edit.gff
chr1	bed2gff	feature	823401	825999	0	+	.	group1;
chr1	bed2gff	feature	927001	928999	0	+	.	group2;
chr1	bed2gff	feature	1048201	1050799	0	+	.	group3;
chr1	bed2gff	feature	1264401	1266799	0	+	.	group4;
chr1	bed2gff	feature	2008801	2011399	0	+	.	group5;
chr1	bed2gff	feature	2185201	2188399	0	+	.	group6;
chr1	bed2gff	feature	2577201	2578999	0	+	.	group7;
chr1	bed2gff	feature	2786201	2789199	0	+	.	group8;
chr1	bed2gff	feature	2923401	2926199	0	+	.	group9;
chr1	bed2gff	feature	3256401	3264399	0	+	.	group10;
Thanks for helping me out!
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Old 12-03-2015, 02:22 AM   #2
Michael.Ante
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Location: Vienna

Join Date: Oct 2011
Posts: 121
Default

Please have a look at the GFF format description (e.g. here). You need to rephrase the last column to ID=group1; ID=group2; ...

Cheers,
Michael
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chip-seq analysis, gff gff2 gff3, htseq-count

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