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Old 01-27-2016, 05:41 AM   #1
Old Pioneer
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Location: Belarus, Minsk

Join Date: Jan 2016
Posts: 1
Default Write the subset of reads from BAM file into new SAM/BAM file, using R tools.

Hello every one.

I am new in bioinformatic, and now I try solve the next problem. I have sorted BAM file with paired-end RNA-Seq data (several tens of thousands reads). My work tool is R. I need: 1) Filter this file by "isize" field: extract the reads with isize not equal to NA and with absolute value of isize lower than threshold (in this case, 642 bp); 2) 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, function filterBam(). Remove reads with isize == NA is possible by means scanBamFlag:
flag <- scanBamFlag(isPaired = TRUE, hasUnmappedMate = FALSE).

But I have no idea about filtration by threshold (abs(bamFile$isize) <= 642). How I can do it in R? I do not believe that effective way for this does not exist. Unfortunately, my experience in R and programming for now is inadequate for solve this problem quickly. Can someone to help me? Thanks in advance!
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