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Question: Warning using feuture count related to GTF file
0
gravatar for roghaiyeh.safari
11 weeks ago by
roghaiyeh.safari0 wrote:

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" 

ADD COMMENTlink modified 11 weeks ago by James W. MacDonald48k • written 11 weeks ago by roghaiyeh.safari0
1
gravatar for James W. MacDonald
11 weeks ago by
United States
James W. MacDonald48k wrote:

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?

ADD COMMENTlink written 11 weeks ago by James W. MacDonald48k
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