test_stat from promoter.diff all zero

[falexandra]

Hi,

I performed a cuffdiff test on Arabidopsis RNA-seq data. I got ~130 genes that are significant in the promoter.diff output.

The confusing thing to me is that, although there is a value for sqrt(JS), the test_stat value is zero for all my genes, although it should be the same as the sqrt(JS) value according to the cuffdiff documentation ("http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#differential-promoter-use---promotersdiff"). I do get p_value and q_value although test_stat is zero.

I ran cufflinks 2.2.0. The gene_exprs.diff output does have a test_stat.

Thanks for any inputs!

[falexandra]

Here is part of the output:

test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
XLOC_006757 XLOC_006757 AT1G57860,AT1G57870 Chr1:21429897-21436810 N KCl OK 0 0 0.218934 0 0.0001 0.0175895 yes
XLOC_000633 XLOC_000633 AT1G13080,AT1G13090 Chr1:4459165-4463543 N KCl OK 0 0 0.237835 0 0.00035 0.0487375 yes
XLOC_030924 XLOC_030924 AT5G55280,AT5G55290 Chr5:22420600-22424411 N KCl OK 0 0 0.252995 0 0.00025 0.0363261 yes
XLOC_008924 XLOC_008924 AT2G17705,AT2G17710 Chr2:7692312-7694824 N KCl OK 0 0 0.267144 0 0.00015 0.0238714 yes
X