Problem with "featurecounts" after MACS2 call peak for ATAC-seq analysis

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1

Hi All,

I running keep getting error while using featureCounts. Here is the message “failed to find the gene identifier attribute in the 9th column of the provided GTF file”

Please helps

Here is entire message

    ==========     _____ _    _ ____  _____  ______          _____  
    =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
      =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
        ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
          ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
    ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
  v2.1.1

//========================== featureCounts setting ===========================\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| dataset_7659bf36-8d17-4929-9e8d-9c266f828a16.dat ||
|| ||
|| Output file : output ||
|| Summary : output.summary ||
|| Paired-end : yes ||
|| Count read pairs : yes ||
|| Annotation : dataset_fc252401-2bc3-415b-b247-fd33aebb57ec … ||
|| Dir for temp files : ./ ||
|| ||
|| Threads : 2 ||
|| Level : meta-feature level ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\============================================================================//

//================================= Running ==================================\
|| ||
|| Load annotation file dataset_fc252401-2bc3-415b-b247-fd33aebb57ec.dat … ||

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 ‘"gene_id ““peak_1"”;”’.

2

Hi @Vu_Ngo,

The error message points on issue with the annotation file and the job setup. featureCount is usually used for gene expression projects, while your annotation file is for peaks. Check this topic:

(ignore my typos, like axon instead of exon)

If this does not help, maybe share the history using the following procedure: click at History Options (three horizontal bars icons) in the top right corner of the History panel; select Share or Publish; in the middle window make the history accessible, copy and paste the link here.

Kind regards,
Igor