counting EXOM reads using subread featureCounts

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3.0 years ago

adR ▴ 120

Hi everyone,

Does anyone know where to download the human Annotating Genomes with GFF3 or GTF files. I want to apply featureCounts to quantify read counts in the bam file in the command line.

featureCounts -t exon -g gene_id -a annotation.gtf -o counts.txt mapping_results_SE.bam

Best,
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featureCounts subread exom • 1.4k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 3.0 years ago by adR ▴ 120

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which organism ? which build ?

ADD REPLY • link 3.0 years ago by Pierre Lindenbaum 164k

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Hi Pierre Lindenbaum,

Thanks for your help! The organism is human and I used hg38 for the alignment.

ADD REPLY • link 3.0 years ago by adR ▴ 120

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Get the annotation file that matches the reference i.e. obtain it from the source where you got the reference from. This will avoid reference name mismatches between annotation and sequence file.

ADD REPLY • link 3.0 years ago by GenoMax 147k

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Please do not post the same content in new threads (EXOM-seq counting ) . Once a thread has received a comment/answer do not delete it.

ADD REPLY • link 3.0 years ago by GenoMax 147k

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okay sorry ---I think I found it here https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml