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
can you specify a bit more what your specific needs are?
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
you could edit your initial question to include all those details
Thanks, I've included that in the initial question.
Aren't
sRNAbench
orCAP-miRSEQ
suitable?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.
Link to sRNAbench stand-alone jar:
http://bioinfo2.ugr.es/sRNAtoolboxDB/exec/sRNAbench.jar
Thanks! I'll try using sRNAbench then.