Help with mapping total RNA reads to human reference but want to keep unmapped reads (with bbmap)

Question

[m.radz]

I am interested in removing host (human) contamination from my total-RNA seq data to retain the unmapped reads for microbial analysis. I am using BBMAP which I have used previously for DNA seq data, but I haven't used it for RNA-seq before.

Looking at the guides it does have a suggestion for doing this, and I have run the program as follows:

bbmap.sh in1=forward_reads.fq in2=reverse_reads.fq outm=mapped.fq outu=unmapped.fq maxindel=200k ambig=random intronlen=20 xstag=us

Is that correct considering what I am aiming to do? I am just interested in the unmapped.fq file in the end.

[GenoMax]

Yes that is correct.

You could have also used the following. This looks for reads that share a kmer with a reference.

bloomfilter.sh in=reads.fq outm=nonhuman.fq outm=human.fq k=31 minhits=3 ref=human.fa

[m.radz]

Would I use that instead of the code I used?