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Novel miRNA identification

Hi!

What are some good open-licensed tools for novel miRNA identification from miRNA-Seq files? I've combed trough tools4mirs.org, but I haven't found something that suits my usecase, since most of them are either dependent on miRDeep2, which is licensed, or aren't quite what I need. I need a tool that has the following feartures:

  • can be used for human sequences

  • can identify novel mature miRNA sequences

  • can handle input read that have miRNA-Seq experimental strategy (but tools that can handle input files with other experimental strategies would be useful as well)

  • has a license that allows non-academic use of the tool

  • doesn't require usage of GUI

Thanks,

Nikola

mirna novel mirna identification mirna-seq
• 3,857 views • link
updated by brianj.park brianj.park • written by tesic93 • tesic93

or aren't quite what I need

can you specify a bit more what your specific needs are?

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written by Friederike Friederike

Sorry, I should have been clearer with the question. I need a tool that can do the following:

  • can be used for human sequences

  • can identify novel mature miRNA sequences

  • can handle input read that have miRNA-Seq experimental strategy (but tools that can handle input files with other experimental strategies would be useful as well)

  • has a license that allows non-academic use of the tool

Thanks!

Nikola

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written by tesic93 • tesic93

you could edit your initial question to include all those details

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written by Friederike Friederike

Thanks, I've included that in the initial question.

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written by tesic93 • tesic93

Aren't sRNAbench or CAP-miRSEQ suitable?

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written by h.mon h.mon

sRNAbench can't be downloaded from their website as far as I know, they had a server crash from which they didn't recover fully.

CAP-miRSEQ seems to use miRDeep2 for alignment, so I can't use it because of miRDeep's academic-only license.

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written by tesic93 • tesic93

Thanks! I'll try using sRNAbench then.

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written by tesic93 • tesic93

2 answers

miRDeep2 is probably the most common software to perform it.

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written by Buffo Buffo

OP has indicated that that program is not suitable for their purpose due to licensing restrictions.

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written by GenoMax GenoMax

In the meantime (on October 16, 2018), miRDeep2 authors added the GNU GPL version 3 to the github repository, so it is now compatible with non-academic use.

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written by h.mon h.mon

You can also give miRge2.0 a try.

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written by brianj.park brianj.park

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