Question: Reference annotation GFT GFF3 problem with tool HISAT
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tran_tim • 10 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]
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modified 2.2 years ago
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Jennifer Hillman Jackson ♦ 25k
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2.2 years ago by
tran_tim • 10
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).
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.