Question: htseq-count unknown error
0
gravatar for mvinas
8 weeks ago by
mvinas10
mvinas10 wrote:

I am trying to use htseq-count tool for gene quantification, but I have this error: "Fatal error: Unknown error occured: Error occured when processing GFF file (line 11 of file /galaxy repl/main/files/018/552/dataset_18552527.dat): Feature id1 does not contain a 'gene_id' attribute [Exception type: ValueError, raised in count.py:53]"

Do I need another input format to use this tool? I use a GFF file (annotated genome).

Thanks, Maria

rna-seq • 105 views
ADD COMMENTlink written 8 weeks ago by mvinas10
1
gravatar for Devon Ryan
8 weeks ago by
Devon Ryan1.3k
Germany
Devon Ryan1.3k wrote:

htseq-count doesn't work with GFF files, only GTF. Try to upload a GTF file (you'll have to manually state that it's GTF when uploading) and rerun things.

ADD COMMENTlink written 8 weeks ago by Devon Ryan1.3k
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