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-   -   Filter cuffcompare by FPKM (http://seqanswers.com/forums/showthread.php?t=48829)

SS00 12-08-2014 03:47 AM

Filter cuffcompare by FPKM
 
How do I filter out low cuffcompare FPKM values out of by combined.gtf file?

I am trying to use the lncrScan workflow for novel long non-coding RNA from total RNA samples. I assembled RABT assembly with cufflinks using combined gtf from UCSC, NCBI and emsembl and then ran cuffcompare on the resulting assembly.

However before I pull out my sequences from the gtf in FASTA format, I want t filter out all transcripts below FPKM of 2. I suppose there could be an awk script for this, but in my combined.gtf there is no FPKM value listed.

Any ideas?

Thanks for the help!

pengchy 04-26-2015 01:03 AM

please take a look at filtercuffcompare from seqscripts: https://github.com/roryk/seqscripts#filtercuffcompare

I have searched around found nobody has used this script here. I have tested this script, filtered plenty of the combined gtf. The rationality is under checking.


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