rRNA remove from RNAseq data

Question

[Peter]

Hi everyone,

I mapped human RNAseq raw data to Refseq rRNA sequences using bwa, it turned out that 20% raw reads mapped to rRNA sequences. Is it normal? But I have used a kit to remove rRNA including cytoplasmic(5s, 5.8s, 18s, 28s) and mitochondrial(12s, 16s) ribosomal RNA. I found that the most mapped reads belong to 45S pre-ribosomal RNA sequences. I have no idea about this. Someone could help me! Any suggestion is welcome!

Thanks!

[Sej Modha]

You could use riboPicker to identify and remove rRNA reads from the fastq files. I am not sure if SILVA databases include the pre-rRNA sequences though.

Answer 1

[firatuyulur]

I have used SortMeRNA before and worked very well for me.

[Shicheng Guo]

SortMeRNA is useful to remove rRNAs. Do you know any option to save these rRNA reads? I want to do some further analysis to these rRNAs. Thanks.

[GenoMax]

You can use bbduk.sh to filter RNA reads and save them. A Guide is here.

Answer 2

[Antonio R. Franco]

There is a program named BBSplit that you can use to filter and remove your undesired sequences

Answer 3

[Dreamer]

There are a number of tools specifically for rRNA reads removal. Recently, we also developed a rRNA reads detection method named RiboDetector (https://github.com/hzi-bifo/RiboDetector), and in the article we benchmarked different computational tools: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac112/6533611. RiboDetector is the most computationally efficient and most accurate software for rRNA reads removal. It can be used out-of-the-box without any database:

• GPU mode:

  ribodetector -t 20 \
  -l 100 \
  -i inputs/reads.1.fq.gz inputs/reads.2.fq.gz \
  -m 10 \
  -e rrna \
  --chunk_size 256 \
  -o outputs/reads.nonrrna.1.fq outputs/reads.nonrrna.2.fq
  

• CPU mode

  ribodetector_cpu -t 20 \
  -l 100 \
  -i inputs/reads.1.fq.gz inputs/reads.2.fq.gz \
  -e rrna \
  --chunk_size 256 \
  -o outputs/reads.nonrrna.1.fq outputs/reads.nonrrna.2.fq
  

[GenoMax]

Please post this as a tool post in a new thread.