feutureCount in the subread
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2.4 years ago
adR ▴ 120

Hello Everyone, I am quantifying read counts in the bam using feutureCount in the command line but getting errors below

ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
The specified gene identifier attribute is 'gene_id'
An example of attributes included in your GTF annotation is 'ID=exon-NR_046018.2-1;Parent=rna-NR_046018.2;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HGNC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1 (pseudogene);pseudo=true;transcript_id=NR_046018.2'
The program has to terminate

I downloaded the reference genome and the annotation files for human from this link below

https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml

and also I used the code below

 featureCounts -t exon -g gene_id -a GRCh38_latest_genomic.gff -o counts.txt 3.bam

I am not sure what is the problem. May I get your help please? .Best, Ad

fe subread • 772 views
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Use -g gene.

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