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rajewsky-lab / mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data
GNU General Public License v3.0
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Output bed files (press, mature and star) have the same coordinates #46

Closed LliliansCalvo closed 4 years ago

LliliansCalvo commented 4 years ago

Hi, After running mirdeep2 and predicting microRNAs I've realised the 3 bed files have exactly the same positions:

examples: mature bed file LQNS02278089.1 848170 848230 LQNS02278089.1_34108 2249659.3 - 848170 848230 0,0,255 LQNS02278089.1 847652 847711 LQNS02278089.1_34106 1566285.5 - 847652 847711 0,0,255

precursor bed file LQNS02278089.1 848170 848230 LQNS02278089.1_34108 2249659.3 - 848170 848230 0,0,255 LQNS02278089.1 847652 847711 LQNS02278089.1_34106 1566285.5 - 847652 847711 0,0,255

Therefore I am blocked at this stage. How could I get a bed file containing the coordinates of the mature sequence, or the star sequences, not just the precursor sequences coordinates three times.

Thanks for the help!

Drmirdeep commented 4 years ago

seems like this is not implemented yet. You can use bowtie or perl or python and get the position of the mature and star in the precursor.

Drmirdeep commented 4 years ago

Updated