Extract reads counts with featureCounts
Hello all,
I'm trying to extract reads counts with featureCounts.
I obtained the gtf file from UCSC genome browsers through the command:
wget https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/genes/dm6.ensGene.gtf.gz
I ran the following command to extract reads counts
featureCounts -a dm6.ensGene.gtf -o Male_RNAseq.tx sorted.files/*bam
However, I got error that says
Failed to open the annotation file dm6.ensGene.gtf, or its format is incorrect, or it contains no 'exon' features.
Does anyone know how I can fix this error? I greatly appreciate any help, thank you
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Where did you get your reference genome from? You should get GTF that corresponds to it to keep things simple.
I got it from [https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/genes/]
I downloaded the file and used gunzip to compress the GTF file.
That folder contains just the GTF files. Did you use this genome reference file: https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.fa.gz
note the error message list several different problems, make sure to eliminate each problem: