coordinates mature microRNAs from precursors

Question

[Amaranta_Remedios]

Hi,

Recently I predicted MicroRNAs for a new specie using miRDeep2. However, the software only gives you the coordinates of the precursors, not the mature and star sequences. I was wondering if you have any suggestion about how to obtain these specific coordinates (mature/star).

Thanks in advance, I'm looking forward to your answers or suggestions.

Answer 1

[h.mon]

You can blast the mature / star to the precursors, and then do some math to get their coordinates.

But I think it is worth opening an issue at the miRDeep2 github page, as the bed files from precursors, mature and star are identical.

In fact, this apparently has been fixed in the latest version, miRDeep2 0.1.3. A similar issue has been marked as corrected, and the releases page says:

• adjusted BED output to include 5p and 3p arms

[Amaranta_Remedios]

Got it ! I will run mirdeep2 again. Thanks