Small Rna (Mirna) Mapping

Question: Small Rna (Mirna) Mapping

9.1 years ago by

Sara • 170

Sara • 170 wrote:

Hello,

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

Thanks Sara

small rna mapping • 6.6k views

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modified 6.5 years ago by Lorena Pantano • 360 • written 9.1 years ago by Sara • 170

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ADD REPLY • link written 9.1 years ago by Jeremy Leipzig ♦ 19k

9.1 years ago by

Fred • 750

Paris, France

Fred • 750 wrote:

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 written 9.1 years ago by Fred • 750

9.1 years ago by

Cjt • 370

Cjt • 370 wrote:

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 written 9.1 years ago by Cjt • 370

i think you meant -n 0

ADD REPLY • link written 9.1 years ago by Doctoroots • 790

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

ADD REPLY • link written 9.1 years ago by Cjt • 370

9.1 years ago by

Rm ♦ 8.0k

Danville, PA

Rm ♦ 8.0k wrote:

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

ADD COMMENT • link written 9.1 years ago by Rm ♦ 8.0k

6.5 years ago by

Lorena Pantano • 360

Barcelona

Lorena Pantano • 360 wrote:

Hi,

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

http://lorenapantano.wordpress.com/2014/02/28/mirna-annotation-tools-which-is-the-best/

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 help.

ADD COMMENT • link written 6.5 years ago by Lorena Pantano • 360

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