counting EXOM reads using subread featureCounts
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,
ad
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which organism ? which build ?
Hi Pierre Lindenbaum,
Thanks for your help! The organism is human and I used hg38 for the alignment.
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.
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.
okay sorry ---I think I found it here https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml
Then download the GFF3 file that is linked on the same page.