Question: Extracting Unmapped Reads from BAM files using Rsamtools
gravatar for danekhoffman0319
4 weeks ago by
danekhoffman03190 wrote:


Does anyone have any experience extracting unmapped reads from BAM files and converting them back to fastq format using Rsamtools? If you could provide some generic code to address this problem it would be greatly appreciated.

I am mapping C. elegans RNA library against E. coli genome to remove contamination. I would like to obtain the unmapped reads to then map against C. elegans genome for DGE.

PS. These are unpaired reads


ADD COMMENTlink modified 4 weeks ago by Shalu Jhanwar400 • written 4 weeks ago by danekhoffman03190

Posting an alternate solution. You can take a look at from BBMap suite. You can easily bin reads by aligning to both these genomes at the same time.

ADD REPLYlink written 4 weeks ago by genomax87k

You can also use GenomicAlignments to pull the unmapped reads out. You really gotta wrangle the metadata and pull all the right values to extract the necessary information to recreate the original fastq lines - but it is do-able.

Example for single end:

ADD REPLYlink written 4 weeks ago by benformatics1.8k
gravatar for Shalu Jhanwar
4 weeks ago by
Shalu Jhanwar400
Shalu Jhanwar400 wrote:

You can use SAM flag value 4 to get reads unmapped from BAM files like below:

samtools view -f 4 in.bam > out.bam

You can provide this flag with Rsamtools as well.

ADD COMMENTlink written 4 weeks ago by Shalu Jhanwar400
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