featureCounts

Question

[Hien]

Helllo, I would like to ask the questions related to featureCounts. I already had the annotation file as .gff3 file. I want to count read pairs for annotated genes based on exons using featureCounts and save the resulting count as .bed file. I wrote the command as below: featureCounts -g genes -t exons -a gencode.annotation.chrX.gff3 -o quantification_genes.bed

The problems are: -my output file always show as: temp_core_00C2932.sam. It is sam file, not bed file as I expected. -my output file always does not show any information of counting.

Could anyone suggest me what is exactly wrong in my command?

Answer 1

[Rogerio Ribeiro]

I'm assuming you are providing an input files to your command and have omitted in above.

Check if you have enough space, I suspect featuresCounts might be trying to store and intermediary sam files (from your encoded bam file) and crashes because it runs out of space. Are there any other outputs in the command line?