Featurecounts error - RNA seq data

I am running Featurecounts for Desulfovibrio alaskensis RNA seq data. I am stuck with the following error.

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’

Could anyone help me with this?

Hi @jawaharrajk

Check your reference annotation (GTF) dataset. Does it have that attribute in the 9th column? For all rows? No headers?

If not, you’ll need to source and format a GTF that works with this tool (and many others).

FAQ: Datatypes - Galaxy Community Hub

You can also click on the tags I added for prior Q&A about this with context.


I was able to fix the featurecounts error and now I have an error in deseq2. Below is the error. It would be great if you could help me with this.

Fatal error: An undefined error occurred, please check your input carefully and contact your administrator.

Tool generated the following standard error:

estimating size factors
estimating dispersions
Error in checkForExperimentalReplicates(object, modelMatrix) : 

  The design matrix has the same number of samples and coefficients to fit,
  so estimation of dispersion is not possible. Treating samples
  as replicates was deprecated in v1.20 and no longer supported since v1.22.

Calls: DESeq ... estimateDispersions -> .local -> checkForExperimentalReplicates

Thank you