featureCounts - ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file

Question

[pavelasquezv]

I am running the featureCounts function but I have the following error

ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file. I downloaded the .gff formats from the NCBI.

featureCounts("G:/Miunidad/Backup_PCacer_28_11_2020/R/3NGS144_S72_L007.Aligned.out.bam", annot.ext="G:/Mi unidad/Backup_PCacer_28_11_2020/R/genomic.gtf")

Please could someone help me with this error

Many thanks, Alex

Answer 1

[Istvan Albert]

According to featureCounts your genomic.gtf file is not a valid GTF file.

Every line needs to have gene_id and transcript_id attribute in the 9th column, it seems that is not true.

[pavelasquezv]

Thanks my friend,

I found the error. It was some wrong in my script.

All the best Alex

[cpad0112]

Not necessary to have gene_id and transcript_id attribute in the 9th column. It can be any feature (attribute), as I understand, in the 9th column. It is just that by default featurecounts takes gene_id as option to -g. If user provides whatever is present in the 9th column with -g option, featurecounts would summarize reads by that feature.