best STAR options for miRNA mapping?
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7.3 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 • 4.8k views
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Why not use bowtie v.1 (fast, ungapped alignments) which may be more appropriate in this case.

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

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7.3 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:

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miRge link does not work

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

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