Getting Counts From Samtools

Question

[Raygozak]

I have the result from aligning illumina reads to a reference genome and i'm able to get the counts per mapped read, however it outputs chromosome name starting position , the end result i want is to replace this information with the actual gene/mrna name that's contained in a gff file for the reference sequence, i haven't found a tool that does this. does such thing exist?

[Damian Kao]

You really need to clarify your question. It sounds like you want to get read count per annotation in the GFF file? What do you mean you already have the 'counts from a BAM files per read'?

Answer 1

[Sean Davis]

Just guessing what you want, but you'll want to take a look at, for example:

• BEDtools
  
• HTSeq
• cufflinks

If you are an R/Bioconductor user, take a look at the GenomicFeatures and GenomicRanges packages.