featureCounts for multiple features
Edward Wallace
I'd like to add to requests that featureCoutns can count across multiple kinds of features, as discussed here:
https://support.bioconductor.org/p/110807/
There are many use-cases beyond counting exons. I am starting with the same use-case, where I want to count reads on five_prime_UTRs, three_prime_UTRs, and CDSs. Also one might want to count reads on exons and introns from the same file. Or might want to count reads on many different kinds of non-coding RNA in the same annotation (snRNA,tRNA, etc). Or on promoters vs transcripts.
Instead of these lines of code (taken from the bioconductor support):
featureCounts -t CDS -g gene_id -a $GTF -o counts.txt $BAM
featureCounts -t five_prime_UTR -g gene_id -a $GTF -o counts.txt $BAM
featureCounts -t three_prime_UTR -g gene_id -a $GTF -o counts.txt $BAM
We want this:
featureCounts -t CDS,five_prime_UTR,three_prime_UTR -g gene_id -a $GTF -o counts.txt $BAM
Surely this would be easy to fix? Instead of passing a single string to the -t argument and filtering by that, pass a character vector/list of strings and filter for inclusion?
I appreciate that the gff-fix workaround you propose in the above support issue works in principle, but it would be far better to add the capability to the software.
Thank you for making a great piece of software and for sharing it with the community! It is fast, effective, and well-documented. I'm a new user.
Best wishes,
Edward Wallace
https://ewallace.github.io/
