Question

Small Rna (Mirna) Mapping

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12.3 years ago

Sara ▴ 170

Hello,

I want to align the small RNA seq from illumina. is BWA a good mapper for small RNA?

Thanks Sara

small rna mapping • 8.4k views

ADD COMMENT • link updated 2.3 years ago by Ram 43k • written 12.3 years ago by Sara ▴ 170

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ADD REPLY • link 12.3 years ago by Jeremy Leipzig 22k

Ram · Answer 1 · 2012-01-10

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12.3 years ago

Fred ▴ 780

I used to align with bowtie, but it should be fine. Moreover, you'd better remove the adapter sequences before the alignment. Hope this helps.

ADD COMMENT • link updated 2.3 years ago by Ram 43k • written 12.3 years ago by Fred ▴ 780

Ram · Answer 2 · 2012-01-09

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12.3 years ago

Cjt ▴ 370

It is working fine when using a lowered seedlen (e.g. "-l 5"). Depending on your data you might decide to accept perfect hits only ("-v 0").

ADD COMMENT • link updated 2.3 years ago by Ram 43k • written 12.3 years ago by Cjt ▴ 370

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i think you meant -n 0

ADD REPLY • link 12.3 years ago by Doctoroots ▴ 800

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Oh, I am sorry! I thought she had been be asking for bowtie... Thanks for correcting me, doctoroots.

ADD REPLY • link 12.3 years ago by Cjt ▴ 370

Ram · Answer 3 · 2012-01-24

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12.3 years ago

Rm 8.3k

Try mirdeep2 (internally it uses Bowtie) or miRNAKey (internally it uses bwa) for aligning to mirbase or complete genome...

ADD COMMENT • link updated 2.3 years ago by Ram 43k • written 12.3 years ago by Rm 8.3k

Ram · Answer 4 · 2014-09-11

Hi,

It depends what you want to detect. Here you have a comparison of tools to detect mirna.

I am currently working in isomirs accuracy, but use miraligner if you want to look to isomirs. (you will find the links in the post)

If you want to detect as much as possible, I would use miraligner for mirnas. For the rest of small RNAs, I am doing a comparison between seqcluster and srnabench, but not finished yet. I have to say that at least with seqcluster you can determine better difference between groups, for instance and take into account multi-mapped reads. You can use any aligner you want that produece SAM format. I would go for bowtie2, gem or bwa.

Hope this helps.