Question: BAM file processing in chunks in R
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gravatar for Tobias
2.1 years ago by
Tobias140
Tobias140 wrote:

When I want to process a FASTQ file in chunks in R, I can use the "FastqStreamer" function from the Bioconductor package "ShortRead".

Is there an analogous function for BAM files (for instance, in the "Rsamtools" package)? If so, could you give some toy code?

Many thanks for your help in advance!

sequencing rna-seq R • 1.1k views
ADD COMMENTlink modified 2.1 years ago by ivivek_ngs4.8k • written 2.1 years ago by Tobias140
0
gravatar for ivivek_ngs
2.1 years ago by
ivivek_ngs4.8k
Seattle,WA, USA
ivivek_ngs4.8k wrote:

Have you tried to read the entire vignette of Rsamtools? There is a function call scanBam. Take a look at this link.

Alternatively if you already have bam chunks for specific chromosomes which you can obtain by splitting the total bams for each chromosomes and then process with scanBAM. Take a look at this SO link.

Splitting bam files in bash

Split with samtools

Bioconductor For Large Bam File Analysis

ADD COMMENTlink written 2.1 years ago by ivivek_ngs4.8k
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