Entering edit mode
7.6 years ago
dr.genetics
▴
60
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?
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"?
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.
You're looking for featureCounts.
What software would you recommend, then?
Thanks a lot.
featureCounts. That is the name of the software :-)
OK, thank you! :) It's odd those popular tools such as samtools cannot do it, though.
The unix philosophy is to write programs that do one thing and do it well. Samtools nicely largely adheres to that.
No it isn't :p Why would it incorporate all possible downstream applications?