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Old 01-18-2012, 08:24 PM   #1
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Location: Durham, NH

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

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

cufflinks -p8 -m320 -u -o /media/hd/working/tuco/17Jan12socialcuff -L social \
--upper-quartile-norm --max-mle-iterations 20000 \

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

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/401C.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??
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Old 01-19-2012, 07:57 AM   #2
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I should note that 'social.bam' is just a product of samtools merge for all the individuals in the social treatment.. Those bamfiles are listed individually in Cuffdiff-- to indicate that there are biological replicates.

So, in essence, the FPKM from social.bam from cufflinks should be the average value from all the individuals in that group.
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Old 01-25-2012, 10:09 AM   #3
Location: New York, NY

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Just at first glance, in your cufflinks run you specify two different parameters that will affect the FPKM calculation.
--upper-quartile-norm --max-mle-iterations 20000
I would try changing --max-mle-iterations to match cuffdiff, disabling quartile normization, and running the biological replicates through cufflinks separately to see if this difference is true. Then I would try cufflinks with the merged BAMs. Internally the same code does the quantification in both cufflinks and cuffdiff.

Also, I noticed you're looking in transcripts.gtf for cufflinks and gene_exp.diff for cuffdiff. It would be better to look in isoforms.fpkm_tracking for both cufflinks and cuffdiff, as gene_exp.diff lists quantification at the locus level while transcripts.gtf is at the isoform level.
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Old 01-25-2012, 07:21 PM   #4
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also, I just realized that log10(1630419.4581286784) is about 6, which is pretty close to 10.. I wonder if the difference is this easy.
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Old 04-18-2012, 04:17 AM   #5
Location: Sheffield, UK

Join Date: Dec 2011
Posts: 32

Did you ever find a solution to this? We run into the same problem.

Our pipeline is thus:
We map reads with tophat for each sample
Run cufflinks on each sample to generate a transcriptome assembly

the command looks something like:
 cufflinks --label tax-Pre-R5
               --num-threads 4
               --library-type fr-secondstrand
               --frag-bias-correct /ifs/mirror/genomes/bowtie/hg19.fa
Run Cuffmerge and Cuffcompare to generate merged gene sets.

We also run cuff diff to test for differences.

Our cuffdiff commands look like:

 cuffdiff --output-dir abinitio.cuffdiff.dir             
                 --library-type fr-secondstrand
                 --frag-bias-correct /ifs/mirror/genomes/bowtie/hg19.fa
                 --num-threads 16
                 --labels Prostate-Pre-agg,Prostate-Post-agg,tax-Pre-agg,tax-Post-agg              
                 --FDR 0.050000
If we compare the FPKMs coming out of cuffcompare and cuffdiff they are not even within two or three orders of magnitude of each other, with the cuffcompare FPKMs being in the millions or tens of millions, while the cuffdiff outputs being in the more sensible 0 - several hundred range.

We're using cufflinks 1.3.1.
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Old 08-01-2012, 07:49 AM   #6
Location: Granada, Spain

Join Date: Dec 2009
Posts: 12


we had the same problem and tried the new Cufflinks version 2.0.2 and it seems the values from Cufflinks and Cuffdiff are the same (have to check it more carefully)

these are the commands I used

cufflinks -o ./Sample001_cufflinks_out_No_N_2.0.2 -u -g ../genes.gtf -p 2 --total-hits-norm ../Sample_001_accepted_hits.bam
cuffdiff -o ./COMPARISON1_SAMPLE1_SAMPLE1BIS_cuffdiff_out/ -L SAMPLE1,SAMPLE1BIS -p 2 -u -v -emit-count-tables -total-hits-norm ../Sample001_cufflinks_out/transcripts.gtf ../Sample_001_accepted_hits.sam ../Sample_001_bis_accepted_hits.sam
I know it's weird to use cuffdiff to compare one sample to itself but I had no other choice...



EDIT: Though the FPKM values from Cufflinks and Cuffdiff are now more similar I still get unreasonable high FPKM values specially for very short genes (around 37nt, regulatory RNAs I guess). Searching for some kind of explanation I found this thread it's worth reading it, good explanation by Cole Trapnell on why in small genes you can get extremely high FPKM values

Last edited by mmanrique; 08-04-2012 at 07:25 AM.
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Old 10-17-2012, 01:07 PM   #7
Location: uk

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Posts: 56

hi all, i had the same prob and i was told to run cuffdiff WITHOUT the "N" option (perform quartile normalization)

hope it helps....
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cuffdiff, cufflinks

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