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Old 12-08-2014, 04:47 AM   #1
SS00
PhD Student
 
Location: La Jolla

Join Date: Jun 2012
Posts: 33
Default 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!
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Old 04-26-2015, 02:03 AM   #2
pengchy
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Location: China

Join Date: Feb 2009
Posts: 116
Default

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.

Last edited by pengchy; 04-26-2015 at 03:08 AM.
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cuffcompare, lncrscan, novel rna

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