I have generated RPKM values for the same dataset using Cufflinks (single input BAM file) and using Cuffdiff where my datasert is part of a larger set of samples (multiple input BAM files). The commands are as follows:-
I have noticed that when I compare RPKM values for individual genes (genes.fpkm_tracking file), the RPKM values generated by the two programs are different even though the input BAM file is the same, for example:-
Gene 1
Cufflinks RPKM 1138.91 (confidence intervals 1130.66,1147.16)
Cuffdiff RPKM 1572.47 (confidence intervals 637.99,2506.94)
Gene 2
Cufflinks RPKM 58.15 (confidence intervals 56.40,59.89)
Cuffdiff RPKM 78.99 (confidence intervals 39.83,118.15)
Can anyone explain this please?
PHP Code:
cufflinks -b /path/to/BowtieIndex/genome.fa -p 8 --max-bundle-frags 100000000 -G /path/to/genes.gtf sample1.bam
PHP Code:
cuffdiff -b /path/to/BowtieIndex/genome.fa -p 8 --max-bundle-frags 100000000 /path/to/genes.gtf sample1.bam sample2.bam sample3.bam sample4.bam sample5.bam sample6.bam
Gene 1
Cufflinks RPKM 1138.91 (confidence intervals 1130.66,1147.16)
Cuffdiff RPKM 1572.47 (confidence intervals 637.99,2506.94)
Gene 2
Cufflinks RPKM 58.15 (confidence intervals 56.40,59.89)
Cuffdiff RPKM 78.99 (confidence intervals 39.83,118.15)
Can anyone explain this please?
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