I have a pair of RNA fastq files that are heavily contaminated with rRNA sequences, to such extent that almost one half of reads originate from a 10K long sequence of reference. I want to remove these reads, and I know I can do it at BAM level in one of many ways (ike Samtools View), but I am curious if there is an efficient way of removing those reads at the fastq stage. The idea is to speed up the alignment in some way.
Is that a good way to remove unwanted reads prior to alignment, in order to speed up the processing? Maybe a trimming tool, or such?
1 answer
The most efficient way would be alignment-free kmer-matching. To do that, you can remove all reads containing ribosomal kmers with BBDuk (where ref is the ribosomal sequence of this organism):
bbduk.sh in1=r1.fq in2=r2.fq out1=clean1.fq out2=clean2.fq ref=ribo.fa k=31 mm=f
You can alternatively gather a set of kmers that are present in ribosomal sequence but not in the rest of the genome and use that, but it's more complicated and probably not necessary.
To make this clear to future readers, BBDuk is open-source, available here, and free for all uses.
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