Extract reads counts with featureCounts

Question

[vivek]

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

[vivek]

[GenoMax]

Where did you get your reference genome from? You should get GTF that corresponds to it to keep things simple.

[vivek]

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.

[GenoMax]

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

[Istvan Albert]

note the error message list several different problems, make sure to eliminate each problem:

1. do you really have a file there?
2. does it have exon features (it should)
3. have your BAM files been aligned to the sequences named the same way as your features