Question

best STAR options for miRNA mapping?

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7.8 years ago

jonessara770 ▴ 240

Hello,

I am a newbie in STAR. my questions:

Do you use STAR for mapping miRNA?

can you share the command lines that you use to map miRNA sequence to mirbase or genome?

Thanks

RNA-Seq • 5.0k views

ADD COMMENT • link updated 7.8 years ago by igor 13k • written 7.8 years ago by jonessara770 ▴ 240

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Why not use bowtie v.1 (fast, ungapped alignments) which may be more appropriate in this case.

ADD REPLY • link 7.8 years ago by GenoMax 148k

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thanks! do you have best options for mirna mapping with bowtie?

ADD REPLY • link 7.8 years ago by jonessara770 ▴ 240

score 1 · Answer 1 · 2017-03-22

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7.8 years ago

igor 13k

Most RNA-seq tools aren't really designed for very short sequences that you get from small RNA-seq. You should look into miRNA-specific tools, such as:

miRge - https://baraslab.github.io/miRge/
miRDeep2 - https://www.mdc-berlin.de/8551903/en/
miRExpress - http://mirexpress.mbc.nctu.edu.tw/

ADD COMMENT • link 4.6 years ago by igor 13k

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miRge link does not work

ADD REPLY • link 4.6 years ago by Ömer An ▴ 260

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Thanks for reporting. I guess things change in 3 years. Now fixed.

ADD REPLY • link 4.6 years ago by igor 13k