Extract reads counts with featureCounts
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7 weeks ago
vivek • 0

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

RNAseq BAM subread featureCounts • 346 views
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Where did you get your reference genome from? You should get GTF that corresponds to it to keep things simple.

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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.

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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

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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
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