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How to detect rRNA from reads ?

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.

next-gen sequencing rna-seq
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written by prpadi • prpadi

What organism are you studying?

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written by Jason Jason

Mainly sequences from Anopheles

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written by prpadi • prpadi

1 answer

I've used SortMeRNA with good effect before.

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updated by Ram Ram • written by cts cts

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.

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written by Shicheng Guo Shicheng Guo

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.

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written by qiyangqd • qiyangqd

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