Question: rRNA remove from RNAseq data
0
gravatar for Peter
19 months ago by
Peter0
Peter0 wrote:

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!

rna-seq • 2.4k views
ADD COMMENTlink modified 19 months ago by ATpoint29k • written 19 months ago by Peter0
1

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.

ADD REPLYlink modified 19 months ago • written 19 months ago by Sej Modha4.6k
1
gravatar for firatuyulur
19 months ago by
firatuyulur300
firatuyulur300 wrote:

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

ADD COMMENTlink written 19 months ago by firatuyulur300

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.

ADD REPLYlink written 14 days ago by Shicheng Guo8.1k

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

ADD REPLYlink written 14 days ago by genomax78k
0
gravatar for Antonio R. Franco
19 months ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.3k wrote:

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

ADD COMMENTlink written 19 months ago by Antonio R. Franco4.3k
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