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:
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:
Thanks for helping me out!
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]
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;
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