SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   htseq-count failure parsing GFF attribute line (http://seqanswers.com/forums/showthread.php?t=64650)

pshah 12-02-2015 02:34 PM

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!

Michael.Ante 12-03-2015 01:22 AM

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


All times are GMT -8. The time now is 12:36 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.