How to detect rRNA from reads ?

Question

[prpadi]

Hi all,

I have sequenced many RNA and I would like to identify all the ribosomal RNA, or a maximum of all of them. Which software could I used to detect these rRNA ?

Thank you for your help.

[Jason]

What organism are you studying?

[prpadi]

Mainly sequences from Anopheles

Answer 1

[cts]

I've used SortMeRNA with good effect before.

[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.

[qiyangqd]

You can refer to the manual which says that for paired-end reads, either paired_in or paired_out can save rRNA to an "aligned.fastq" file, depending on your purposes.