Question: Subsetting data from BAM file using R tools
gravatar for Ilya IN
4.7 years ago by
Ilya IN0
Belarus/Minsk/Belarusian State University
Ilya IN0 wrote:

Good day to all! This is my first  post in Biostars.

I have BAM file with Paired-End RNA seq reads, and I need filter this file by "isize" field: extract the reads with isize not equal to NA and with absolute value of isize lower than treshold (in this case, 642 bp). After all, I must write this subset into SAM file (because this type is required for package which I will use).

I tried use R package Rsamtools for this, but my experience in R is inadequate for solve this problem quickly. If I'm right, settings "param" of function filterBam() can help (if I get BAM file with targer subset, I'll use asSam() to convert into SAM format). Remove reads with isize == NA is possible by means scanBamFlag:

flag <- scanBamFlag(isPaired = TRUE, hasUnmappedMate = FALSE)

But I have no idea about filtration by treshold (abs(bamFile$isize) <= 642). How I can do it in R?

Thanks in advance for your help!

myposts rna-seq R • 1.9k views
ADD COMMENTlink modified 4.7 years ago by karimse0720 • written 4.7 years ago by Ilya IN0
gravatar for karimse07
4.7 years ago by
karimse0720 wrote:

you can use pmax function in R for athreshold

ADD COMMENTlink modified 9 months ago by RamRS30k • written 4.7 years ago by karimse0720

I don't see pmax working in this case!

ADD REPLYlink written 4.7 years ago by Sukhdeep Singh10k

Thank you for answer, but how it can help me with BAM file subsetting? Can you give an example?

ADD REPLYlink written 4.7 years ago by Ilya IN0
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