Warning using feuture count related to GTF file
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@roghaiyehsafari-17400
Last seen 3.9 years ago

I try to read counts using featurecounts and I have a warning says:

could somebody help me to figureout the problem?

 

Warning: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
The specified gene identifier attribute is 'gene-id'
The attributes included in your GTF annotation are 'gene_id "ENSOARG00000017577"; gene_version "1"; transcript_id "ENSOART00000019126"; transcript_version "1"; exon_numbe                                          r "1"; gene_name "ING5"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "ING5-201"; transcript_source "ensembl"; transcript_biotype "protein_coding                                          "; exon_id "ENSOARE00000174320"; exon_version "1";'

||    Features : 239130                                                       ||
||    Meta-features : 1                                                       ||
||    Chromosomes/contigs : 702                                               ||
||                                                                            ||
|| Process BAM file resultsAligned.sortedByCoord.out.bam...                   ||
||    Paired-end reads are included.                                          ||
||    Assign reads to features...                                             ||
||    Total reads : 33880102                                                  ||
||    Successfully assigned reads : 12941327 (38.2%)                          ||
||    Running time : 0.96 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
|| Summary of counting results can be found in file "counts.txt.summary" 

featurecounts • 2.5k views
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@james-w-macdonald-5106
Last seen 3 hours ago
United States

The warning says

failed to find the gene identifier attribute in the 9th column of the provided GTF file.
The specified gene identifier attribute is 'gene-id'

And then it (very helpfully, IMO) then says

The attributes included in your GTF annotation are 'gene_id "ENSOARG00000017577"; gene_version "1";

Which just so happens to be the default, indicating that you have over-ridden the default argument for GTF.attrType of "gene_id", with "gene-id". Unless you have a good reason for doing so, your best bet is to stick with the default arguments. And while not all warnings are clear, I'm not sure this one is that hard to figure out?

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