Question: Novel miRNA identification
0
gravatar for tesic93
2.1 years ago by
tesic9310
tesic9310 wrote:

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

ADD COMMENTlink modified 6 weeks ago by brianj.park20 • written 2.1 years ago by tesic9310

or aren't quite what I need

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

ADD REPLYlink written 2.1 years ago by Friederike5.4k

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

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by tesic9310
1

you could edit your initial question to include all those details

ADD REPLYlink written 2.1 years ago by Friederike5.4k
1

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

ADD REPLYlink written 2.1 years ago by tesic9310

Aren't sRNAbench or CAP-miRSEQ suitable?

ADD REPLYlink written 2.1 years ago by h.mon29k

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.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by tesic9310
1

Link to sRNAbench stand-alone jar:

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

ADD REPLYlink written 2.1 years ago by h.mon29k

Thanks! I'll try using sRNAbench then.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by tesic9310
1
gravatar for Buffo
2.1 years ago by
Buffo1.8k
Buffo1.8k wrote:

miRDeep2 is probably the most common software to perform it.

ADD COMMENTlink written 2.1 years ago by Buffo1.8k
1

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

ADD REPLYlink written 2.1 years ago by genomax80k

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.

ADD REPLYlink written 7 weeks ago by h.mon29k
0
gravatar for brianj.park
6 weeks ago by
brianj.park20
Montréal, Canada
brianj.park20 wrote:

You can also give miRge2.0 a try.

ADD COMMENTlink written 6 weeks ago by brianj.park20
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