Question: How to map BAM/SAM files to genes with abundance levels?
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gravatar for dr.genetics
2.4 years ago by
dr.genetics50
dr.genetics50 wrote:

I am a newbie to NGS, and this question might seem to be naiive.

I have a set of SAM files from DNA seq, and I simply want to convert them to genomic coordinates and distance to genes and also the abundance levels of the seqs. What's the best tool to do so?

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by dr.genetics50

There seems to be some disconnect between the title of this post and the content (or perhaps just a difference in terminology). DNAseq you are referring to is data that came from RNA (which was converted to DNA before sequencing)? So are you asking to get the genomic coordinates for regions that have reads present (not sure what this means "convert them to genomic coordinates and distance to genes"?

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by genomax62k

You are right, I made a mistake on the title. Will make a change immediately after this reply.

The genomic coordinates are already in the BAM/SAM files, but I also want them to be in the final output files as well. Basically, I am looking for a tool to map the seqs in the BAM/SAM files to the closest genes in the genome and also get the abundance levels of the DNA seqs.

ADD REPLYlink written 2.4 years ago by dr.genetics50

You're looking for featureCounts.

ADD REPLYlink written 2.4 years ago by Devon Ryan88k

What software would you recommend, then?

Thanks a lot.

ADD REPLYlink written 2.4 years ago by dr.genetics50

featureCounts. That is the name of the software :-)

ADD REPLYlink written 2.4 years ago by genomax62k

OK, thank you! :) It's odd those popular tools such as samtools cannot do it, though.

ADD REPLYlink written 2.4 years ago by dr.genetics50
1

The unix philosophy is to write programs that do one thing and do it well. Samtools nicely largely adheres to that.

ADD REPLYlink written 2.4 years ago by Devon Ryan88k

No it isn't :p Why would it incorporate all possible downstream applications?

ADD REPLYlink written 2.4 years ago by WouterDeCoster36k
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