BAM-Readcounts or R

[fk566938]

Hello, I am trying to get readcounts of coordinates of a gene I found on ucsc genome browser on some bam files I have. Is there some sort of protocol on how to use either bam-readcounts or "R" to do this quick analysis. I am new to linux and bioinformatics in general.

[GenoMax]

See this thread (an oldie) but should give you what you need: http://sourceforge.net/p/samtools/ma...sage/27419954/

If you want the bare minimum steps (replace chr1:1234-2345 with actual coordinates of your gene, you may have to make sure that chromosome name matches what is in your bam e.g. chr1 vs 1).

$ samtools index input.bam
$ samtools view input.bam chr1:1234-2345 | wc -l

[blancha]

I haven't tried the other suggested methods, but bedtools multicov is extremely fast and simple to use.

http://bedtools.readthedocs.org/en/latest/content/tools/multicov.html

bedtools multicov \
-bams bamFile.bam \
-bed region.bed