What's the sqrt(JS) in the cuffdiff output file"cds.diff"

Question

[Yunlong JIA]

Hi, dear friends,

I have a question about the cds.diff ,which output by cuffdiff.. The term in the tag"sqrt(JS)", I really don;t know what;s the meaning.

`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_000003 XLOC_000003 NM_001005484 chr1:69090-70008 hESC hMSC_AT NOTEST 0 0 0 0 1 1 no XLOC_000006 XLOC_000006 NM_152486 chr1:925740-959299 hESC hMSC_AT NOTEST 0 0 0 0 1 1 no XLOC_000007 XLOC_000007 NM_198317 chr1:960586-965719 hESC hMSC_AT NOTEST 0 0 0 0 1 1 no

`

Just like above, if the result is significant, how could I explain it?

Thank you very much for your help. Yunlong

Answer 1

[Yunlong JIA]

Sorry for my disordered type-setting~ it's better now~

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_000003 XLOC_000003 NM_001005484 chr1:69090-70008 hESC hMSC_AT NOTEST 0 0 0 0 1 1 no

XLOC_000006 XLOC_000006 NM_152486 chr1:925740-959299 hESC hMSC_AT NOTEST 0 0 0 0 1 1 no

XLOC_000007 XLOC_000007 NM_198317 chr1:960586-965719 hESC hMSC_AT NOTEST 0 0 0 0 1 1 no'