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

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

genome annotation database alignment
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updated by cpad0112 cpad0112 • written by pavelasquezv • pavelasquezv

1 answer

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.

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written by Istvan Albert Istvan Albert

Thanks my friend,

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

All the best Alex

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written by pavelasquezv • pavelasquezv

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.

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written by cpad0112 cpad0112

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