Question: Getting all unmapped reads
gravatar for mm4184
13 months ago by
mm418420 wrote:

I have a fastqsanger dataset from an RNAseq experiment, and I am trying to remove contaminating human sequences. I can run BWA for Illumina against the human genome and get BAM files of the mapping, but I am trying to get a fastqsanger file with only the unmapped reads. I have been able get this as a standard output option in other programs, but I can't seem to find out how to do this here. I also tried RNA Star, but it is listed as "new" and it looks to me like no reference genomes are available to it yet.

Thanks for your help.


rna-seq bwa • 828 views
ADD COMMENTlink modified 13 months ago by Guy Reeves1.0k • written 13 months ago by mm418420
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:


All BWA tools at do not offer an option to output fastq datasets of unmapped reads directly. Instead, use tools to filter the mapped BAM result dataset to only include unmapped reads then convert SAM/BAM to fastq. There are a few tools to do the filtering and multiple filtering criteria can be set - including filters to capture low-quality mapping results.

One SAM/BAM filtering tool is in the Picard group along with a tool to convert SAM to FASTQ (it also accepts BAM input). SamTools and BAMtools also have BAM/SAM filtering tools. When using these tools be sure to sort the BAM/SAM dataset first, as a distinct step:

Some of the newer wrappers for mapping tools do include this option, including RNASTAR. RNASTAR is pending indexes, so use a custom genome for now:

The same fastq data generally not appropriate for both BWA and RNASTAR but this may be why you want to capture the unmapped reads in your search for contamination.

Hope this helps! Jen, Galaxy team

ADD COMMENTlink modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson25k
gravatar for Guy Reeves
13 months ago by
Guy Reeves1.0k
Guy Reeves1.0k wrote:

You may want to look at this post which asks a related question

ADD COMMENTlink written 13 months ago by Guy Reeves1.0k
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