Counting Features metaRNA-seq

Question

[jbran]

Hi All,

I am attempting to perform RNA-seq analysis on microbiome transcripts. I have managed to align my transcripts to my reference genomes, but have no idea how to simply count the number of reads per feature. I could write a script, but don't want to reinvent the wheel if it has already been done. At the moment I have a whole bunch of sorted bam files from each of my individual communities. Let me know if any one has any suggestions.

Answer 1

[zorbax]

Have you tried this? -_-

[jbran]

Yes, the problem is I do not have access to a gff file. Since I have a reference database of over 1,00 genomes I am not exactly sure how to go about making one from scratch.