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
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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version 2.3.6
Could you post a few lines so we can see what the output looks like?
https://mathavan-muthaiy.imgbb.com/
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