Filter cuffcompare by FPKM

[SS00]

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]

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.