Question: Counting abundance of each gene in SAM/BAM file
0
gravatar for Hansen_869
6 months ago by
Hansen_86920
Hansen_86920 wrote:

I have just aligned my raw FASTQ-files (from a metagenomic sample) to my predicted genes (I used Prokka) with BWA, in order to get an idea of the abundance of each of the genes in the sample. I now have a SAM and a BAM file. My question is: How do I count the abundance (how many reads are mapped to each gene), of all my genes. I basically want an output in the style of (of course doesn't have to be this exact formatting, but you get the idea):

Gene 1 - Mapped reads: 34

Gene 2 - Mapped reads: 85

and so forth.

I could make a script that would extract and count the mapped reads, but I wonder if there is a tool out there that could do it better?

abundance sam samtools bam gene • 380 views
ADD COMMENTlink written 6 months ago by Hansen_86920
1

Prokka also outputs gff / gtf / bed files, correct? Use featureCounts with the bam and the gtf, read the docs for more details.

ADD REPLYlink written 6 months ago by h.mon29k

Thanks for your response! Porkka only outputs gff files. Is that enough?

ADD REPLYlink written 6 months ago by Hansen_86920

featureCounts should work with gff. Out of curiosity, are the raw fastq files you mapped RNAseq reads?

ADD REPLYlink written 6 months ago by h.mon29k

Cool, I'll check it out! They are DNAseq, Illumina :)

ADD REPLYlink written 6 months ago by Hansen_86920
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