Question: Collecting unmapped RNA-seq reads
0
gravatar for Patrick
10 weeks ago by
Patrick0
Patrick0 wrote:

Dear community,
I used subread-align to map RNA-seq reads to the reference genome (after index building) resulting in SAM files. Now, I am additionally interested in the unmapped reads (not aligning to the reference), but the subread-package seems to only show the number of unmapped reads and is not collecting them.

Questions:
1. Is there a way to collect unmapped reads within the subread-package
2. Otherwise, can you suggest a program able to do this?

Thanks a lot

ADD COMMENTlink modified 10 weeks ago by Wei Shi3.2k • written 10 weeks ago by Patrick0
Answer: Collecting unmapped RNA-seq reads
1
gravatar for Robert Castelo
10 weeks ago by
Robert Castelo2.3k
Spain/Barcelona/Universitat Pompeu Fabra
Robert Castelo2.3k wrote:

I don't know about subread-align but outside BioC, the STAR aligner offers the option --outReadsUnmapped Fastx that will dump the unmapped reads to FASTQ files.

cheers,

robert.

ADD COMMENTlink written 10 weeks ago by Robert Castelo2.3k
Answer: Collecting unmapped RNA-seq reads
1
gravatar for Gordon Smyth
10 weeks ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

The SAM files from Subread contain all the reads, both mapped and unmapped. You can use standard samtools utiliites to extract any subset of reads you want, e.g., mapped or unmapped reads. It should be easy to figure out how to do that from a Google search or from the samtools manual.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Gordon Smyth39k
Answer: Collecting unmapped RNA-seq reads
0
gravatar for Wei Shi
10 weeks ago by
Wei Shi3.2k
Australia
Wei Shi3.2k wrote:

As Gordon said the Subread output includes both mapped and unmapped reads. It is fairly straightforward to extract unmapped reads from a SAM file. The 'RNAME' column (the 3rd column) in the SAM file contains a value '*' for each unmapped read.

ADD COMMENTlink written 10 weeks ago by Wei Shi3.2k
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