How to extract lncRNA from CPC2 output?
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4.7 years ago

Hello All I am working on lncRNA expression in the human system, for the prediction of lncRNA, I used CPC2, Totaly I have 25 samples & all the analysis has done command line. how do I extract non-coding RNA which have greater than 200 nucleotides in length, Please suggest any codes to parse out from the CPC2 output?

Thank you

RNA-Seq Assembly next-gen • 1.6k views
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Could you post a few lines so we can see what the output looks like?

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ID transcript_length peptide_length Fickett_score pI ORF_integrity coding_probability label

SRR6453201.1/1 100 30 0.43207 11.7229614258 -1 0.150595 noncoding SRR6453201.1/2 100 9 0.32852 12.0165405273 -1 0.200103 noncoding SRR6453201.6/1 100 0 0.38946 0.0 -1 0.00272557 noncoding SRR6453201.6/2 100 4 0.37476 5.27496337891 1 1.02323e-05 noncoding SRR6453201.2/1 100 0 0.38486 0.0 -1 1.49274e-05 noncoding SRR6453201.2/2 100 15 0.41036 10.3472290039 -1 0.0911879 noncoding SRR6453201.3/1 100 18 0.42229 9.03497314453 -1 0.0428612 noncoding SRR6453201.3/2 100 0 0.39303 0.0 -1 0.003208 noncoding SRR6453201.8/1 100 26 0.39482 9.78216552734 -1 0.0833799 noncoding SRR6453201.8/2 100 14 0.43918 7.99981689453 -1 0.0217406 noncoding SRR6453201.7/1 100 19 0.35534 7.97601318359 -1 0.0511219 noncoding SRR6453201.7/2 100 7 0.44667 4.02764892578 -1 0.0132876 noncoding SRR6453201.5/1 100 29 0.38882 8.00030517578 -1 0.0373591 noncoding SRR6453201.5/2 100 2 0.39131 5.27496337891 -1 0.00956335 noncoding SRR6453201.4/1 100 13 0.43496 6.49139404297 1 0.00341016 noncoding SRR6453201.4/2 100 7 0.42424 5.27496337891 1 0.00299868 noncoding SRR6453201.13/1 100 5 0.43126 6.68426513672 -1 0.0120505 noncoding SRR6453201.13/2 100 29 0.41932 6.70184326172 -1 0.0180771 noncoding SRR6453201.9/1 100 14 0.40405 10.3472290039 -1 0.0946753 noncoding SRR6453201.9/2 100 14 0.39329 8.50006103516 -1 0.0396427 noncoding SRR6453201.10/1 100 8 0.42045 3.99884033203 1 0.00670307 noncoding SRR6453201.10/2 100 0 0.43896 0.0 -1 0.0303935 noncoding SRR6453201.14/1 100 17 0.43905 5.22259521484 -1 0.0124461 noncoding SRR6453201.14/2 100 14 0.30609 9.50006103516 -1 0.165237 noncoding

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4.7 years ago

I'd suggest you not to use CPC2 because there are several better performing alternatives out there. I've developed RNAsamba, a software that has the same purpose of CPC2 with a much higher classification performance. You can use it online here: https://rnasamba.lge.ibi.unicamp.br/

As for your question, are you using the command line? If so, you can filter the output (of both RNAsamba and CPC2) using grep:

grep "noncoding" output.tsv

If you're not experienced with the command line, you can open the output file in Excel and filter it there.

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