Question: Small Rna (Mirna) Mapping
0
gravatar for Sara
7.5 years ago by
Sara160
Sara160 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 • 5.8k views
ADD COMMENTlink modified 4.9 years ago by Lorena Pantano360 • written 7.5 years ago by Sara160

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ADD REPLYlink written 7.5 years ago by Jeremy Leipzig18k
1
gravatar for Fred
7.5 years ago by
Fred720
Paris, France
Fred720 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 COMMENTlink written 7.5 years ago by Fred720
0
gravatar for Cjt
7.5 years ago by
Cjt370
Cjt370 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 COMMENTlink written 7.5 years ago by Cjt370

i think you meant -n 0

ADD REPLYlink written 7.5 years ago by Doctoroots780

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

ADD REPLYlink written 7.5 years ago by Cjt370
0
gravatar for Rm
7.5 years ago by
Rm7.9k
Danville, PA
Rm7.9k wrote:

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

ADD COMMENTlink written 7.5 years ago by Rm7.9k
0
gravatar for Lorena Pantano
4.9 years ago by
Barcelona
Lorena Pantano360 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 COMMENTlink written 4.9 years ago by Lorena Pantano360
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