Question: Getting Counts From Samtools
0
gravatar for Raygozak
7.9 years ago by
Raygozak1.3k
State College, PA, Penn State
Raygozak1.3k wrote:

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?

samtools tophat rna • 2.6k views
ADD COMMENTlink modified 7.9 years ago by Sean Davis25k • written 7.9 years ago by Raygozak1.3k
2

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'?

ADD REPLYlink written 7.9 years ago by Damian Kao15k
1
gravatar for Sean Davis
7.9 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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

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

ADD COMMENTlink written 7.9 years ago by Sean Davis25k
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