Novel miRNA identification
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6.7 years ago
tesic93 ▴ 40

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 • 2.9k views
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or aren't quite what I need

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

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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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you could edit your initial question to include all those details

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

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Aren't sRNAbench or CAP-miRSEQ suitable?

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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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Link to sRNAbench stand-alone jar:

http://bioinfo2.ugr.es/sRNAtoolboxDB/exec/sRNAbench.jar

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Thanks! I'll try using sRNAbench then.

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6.7 years ago
Buffo ★ 2.4k

miRDeep2 is probably the most common software to perform it.

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

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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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4.7 years ago
brianj.park ▴ 60

You can also give miRge2.0 a try.

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