Reading bam files and extratcing transcript from abm files in R

Question

[EVR]

Hi,

I have a to read a bam file into R and extract information related to a particular transcript in bam format. In linux terminal, we can acheive this using

samtools view -bS -F 4 sorted_file.bam transcript_xx > transcript_xx.bam

How can I achieve the same thing within R. Kindly guide me. Thanks in advance

Answer 1

[GouthamAtla]

You should use scanBam function from RSamtools along with GenomicRanges

E.g

what <- c("rname", "strand", "pos", "seq", "qual", "maps")
param <- ScanBamParam(what = what, flag = scanBamFlag(isUnmappedQuery = FALSE))
bam <- scanBam(bam.file, param = param)

Then use GRanges to filter for specific coordinates.

Answer 2

[venu]

First create an object with the above command and execute with system

Ex:

x="samtools view -bS -F 4 sorted_file.bam transcript_xx > transcript_xx.bam"
system(x)

[EVR]

Hi venu,

I am aware of system() command in R. But how can can I store the output of system(x) in bam format in R.