How to count number of reads aligned to rRNA and tRNA in bacterial genome
Hi everybody,
I am trying to find number of reads that are aligned to salmonella rRNA and tRNA genes. I use GenomicAlignment R package for counting reads. It works very well for counting the reads aligned to common genes but when it comes to rRNA and tRNA genes, it can not count them because in the related annotation in NCBI, these genes are not referred as genes. Do anybody have any solution for this or maybe a better tool that can handle this issue?
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Change/add relevant entries for those genes in annotation file you are using.
On a different note: You do not appear to be validating answers for past questions you have posted. Accepting answers (green check mark against the answer, if answer helped you) or up-voting useful comments is the way you show appreciation/validation for effort people put in on this site.