View Single Post
Old 01-18-2012, 08:24 PM   #1
peromhc
Senior Member
 
Location: Durham, NH

Join Date: Sep 2009
Posts: 108
Question cufflinks FPKM >>> Cuffdiff FPKM

I cannot understand why the FPKM estimated in cufflinks is SO much larger than that in cuffdiff:

Cufflinks
Code:
cufflinks -p8 -m320 -u -o /media/hd/working/tuco/17Jan12socialcuff -L social \
--upper-quartile-norm --max-mle-iterations 20000 \
/media/hd/working/tuco/b2.social/social.bam

cat transcripts.gtf | grep 'comp14388_c0_seq1'

comp14388_c0_seq1; FPKM "1630419.4581286784";
I merged the .gtf files from each cufflinks run, and fed that to cufflinks
I have 5 biological reps for each group

Cuffdiff
Code:
mkdir /media/hd/working/tuco/17Jan.cuffdiff
cd /media/hd/working/tuco/17Jan.cuffdiff

cuffdiff -p8 -L social,solitary -N -u \
--max-mle-iterations 10000 /media/hd/working/tuco/17Jan12cuffcompare/*gtf \
/media/hd/working/tuco/b2.bams/406A.bam,\
/media/hd/working/tuco/b2.bams/4262.bam,\
/media/hd/working/tuco/b2.bams/2354.bam,\
/media/hd/working/tuco/b2.bams/4241.bam,\
/media/hd/working/tuco/b2.bams/401C.bam \
/media/hd/working/tuco/b2.bams/6236.bam,\
/media/hd/working/tuco/b2.bams/2226.bam,\
/media/hd/working/tuco/b2.bams/5B5C.bam,\
/media/hd/working/tuco/b2.bams/255D.bam,\
/media/hd/working/tuco/b2.bams/4572.bam

cat gene_exp.diff | grep 'comp14388_c0_seq1'

comp14388_c0_seq1:0-1977	social	solitary	10.5437	8.08172

ok... 1630419.4581286784 >>> 10.5437 Why??
peromhc is offline   Reply With Quote