Question: PITA troubleshooting for miRNA target prediction
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gravatar for luca.marisaldi
4 months ago by
luca.marisaldi30 wrote:

Hy guys, I am trying to run PITA (https://www.nature.com/articles/ng2135) on my own local computer (Ubuntu) for miRNA target prediction.

I've got miRNAs and UTR sequences in .fa format. The program works well with examples provided and with other sequences. However, with such UTR sequences I've got this by running PITA with default options:

Calculating predictions... Reading relations from file tmp_utr_stab_13637 done. Joining on file tmp_prefix_13637 done. Finding potential targets... allowed lengths = 6 7 8 allowed_gu_wobbles{6} = 0 allowed_gu_wobbles{7} = 1 allowed_gu_wobbles{8} = 1 allowed_mismatches{6} = 0 allowed_mismatches{7} = 0 allowed_mismatches{8} = 1 allowed_loops = MicroRNA Names: mmu-mir-101b ola-mir-142 MicroRNA Sequences: TCAGTTATCATGGTACCGGTGC  CCATAAAGTAGGAAACACTACA  1 2 3 Computing site scores... Reading relations from file long_ext_utr.stab done. Joining on file - done.

Computing 51 results: Calling RNAduplex with 51 targets... RNAduplex failure. Result was .(((((((((...((((((.&.))))).)......))))))))). 3 22 25 48 20 24 -16.50 -9.00 -7.50 .(((((((..(((((((((.&.)).)))))))........))))))). 1 20 24 50 20 27 -14.20 -5.00 -9.20 .(((((.((.......(((.&.))).......)).))))). 1 20 31 50 20 20 -7.84 -5.60 -2.24 .(((((((((..((((((.&.)))))...........................)..)).))))))). 1 19 4 50 19 47 -11.42 -8.70 -2.72 ERROR: Wrong constraint given at 3, 48 ERROR: Wrong constraint given at 4, 47 ERROR: Wrong constraint given at 5, 46 ERROR: Wrong constraint given at 7, 44 Done.

I already checked usual things such as format and directories but the fact is that PITA show this bug only with some sequences while runs okay with the rest.

Maybe someone else has already noticed such bug and might help me? Any idea with this problem?

Thank you very much

Luca

target prediction pita mirna • 151 views
ADD COMMENTlink written 4 months ago by luca.marisaldi30
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