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Old 01-20-2014, 04:43 AM   #1
seeker
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Location: Zurich

Join Date: Jan 2011
Posts: 26
Default Weird confidence intervals from Cuffdiff

Hi All,

Something odd seems to be going on with an analysis I'm doing. I have run the tuxedo suite through to using cummerbund but am seeing some genes which have confidence intervals that do not encompass the FPKM value. The whole confidence interval is lower than the actual FPKM (see attached barplot last pair, and fourth from last pair of bars)

Any ideas what's going on here?

command line call and version info:
Code:
 cuffdiff -o diff_out_NA_AA -b Bter_gDNA.fa -p 16 -L NA,AA -u merged_asm/merged.gtf ./tophat_out_CNA/accepted_hits.bam,./tophat_out_DNA/accepted_hits.bam,./tophat_out_ENA/accepted_hits.bam ./tophat_out_CAA/accepted_hits.bam,./tophat_out_DAA/accepted_hits.bam,./tophat_out_EAA/accepted_hits.bam 
version	2.1.1
SVN_revision	4046M
boost_version	104900
Attached Files
File Type: pdf barplot_all.pdf (450.7 KB, 15 views)
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