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Old 02-17-2015, 08:05 AM   #1
Rainbird
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Default Zero fpkm estimation using cuffquant/cuffnorm (Cufflinks 2.2.1)

Hi,

I'm running pre-compiled cuffquant/cuffnorm from cufflinks 2.2.1 on two workstations. Both have tophat-2.0.9, samtools-0.1.19 and bowtie2-2.1.0 installed and specified in $PATH.

The cuffquant/cuffnorm pipeline works just fine on the workstation running CentOS 6.4. However, the other one, which runs CentOS 7, has some problem of estimating normalized expression value. Specifically, it outputs 0 value for every transcripts for some RNA-seq sequencing data.

For the data with error, I tried to move the abundances.cxb file generated by cuffquant from the CentOS 7 workstation to the CentOS 6.4 workstation, and then used the cuffnorm on CentOS 6.4 workstation to re-estimate the normalized expression value, but no luck. However, if I tracked back one more step and moved the accepted_hits.bam from CentOS 7 workstation to the CentOS 6.4 workstation, and did the rest cuffquant/cuffnorm steps on the CentOS 6.4 workstation, it will give out reasonable values. It seems to me that the problem comes from the cuffquant step, but I can't figure it out why.

Any one could help?
Thanks a lot,
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Old 02-17-2015, 11:30 AM   #2
GenoMax
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Consider upgrading the tuxedo suite programs to latest versions (unless you have some specific reason not to). You are using versions that were current as of Mid-2013 which is old is NGS life-cycle terms.
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Old 02-17-2015, 05:46 PM   #3
Rainbird
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It seems that the cuffquant/cuffnorm steps are not included in tuxedo yet.
The good thing about the cuffquant/cuffnorm is that I can do addtional tests based on the normalized expression values.
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