Question: Reference annotation GFT GFF3 problem with tool HISAT
0
gravatar for tran_tim
15 months ago by
tran_tim10
tran_tim10 wrote:

I got the following error while running htseq count: I think it is my gtf file problem. How to fix it?

Fatal error: Unknown error occured Error occured when processing GFF file (line 6 of file /galaxy-repl/main/files/017/359/dataset_17359504.dat): The attribute string seems to contain mismatched quotes. [Exception type: ValueError, raised in __init__.py:161]

hisat format gff3 gtf input • 463 views
ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson23k • written 15 months ago by tran_tim10

Can you post the 6th line of that file in your history (use the "Select first lines from a dataset" tool if you're on the main usegalaxy.org site).

ADD REPLYlink written 15 months ago by Devon Ryan1.9k

chr1 havana gene 11869 14409 . + . "gene_id ""ENSG00000223972""; gene_version ""5""; gene_name ""DDX11L1""; gene_source ""havana""; gene_biotype ""transcribed_unprocessed_pseudogene""; havana_gene ""OTTHUMG00000000961""; havana_gene_version ""2"";"

Above is the the 6th line of the file.

ADD REPLYlink written 15 months ago by tran_tim10
1
gravatar for Devon Ryan
15 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

Eeek, yeah, that file got messed up somehow (all of the ""s are wrong). You should just delete it and download a new copy from Gencode.

ADD COMMENTlink written 15 months ago by Devon Ryan1.9k
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