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:
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
Comment