search

csglab / REMBRANDTS

REMoving Bias from Rna-seq ANalysis of Differential Transcript Stability
GNU General Public License v3.0
13 stars 11 forks source link

stability.filtered.mx.txt Interpretation #12

Open Anna-xu408 opened 10 months ago

Anna-xu408 commented 10 months ago

Hi,I successfully run the pipeline, the stability. The stability.filtered.mx.txt file: GeneID KK_P1 KK_P2 WK_P1 WK_P2 WT_P1 WT_P2 ENSMUSG00000000085.16 -0.231611208842143 -0.164151921085439 0.0247953992771943 -0.0243588348504434 0.0115062163438441 0.0526925217072597 ENSMUSG00000000125.5 -0.0575757926971183 0.0519360127140006 0.240540918361794 0.179097338782403 -0.00779500585753281 -0.0593309187955071 ENSMUSG00000000127.15 -0.0174466268318849 -0.0573737724952284 -0.273639121824414 -0.24207064571395 -0.0948283613103956 -0.0384545849222873 ENSMUSG00000000131.15 -0.0734909090407269 -0.0532761963986637 0.0788007113413504 0.10973382117528 0.123054124377814 0.120821006014771 ENSMUSG00000000167.14 -0.026801290720293 -0.0628139845582957 -0.214523125388475 -0.23605883291347 -0.102359678306202 -0.0562331298110886 But I don't know how to understand the number,What do these numbers mean? Thank you very much

rached-97 commented 10 months ago

Hi Anna,

The numbers in this file can be interpreted as the difference in RNA stability for a given gene in a given sample relative to estimated average stability of that gene across all samples, adjusting for the gene-specific bias introduced by pre-mRNA processing which we describe in this paper https://www.nature.com/articles/s41467-017-00867-z

The numbers are on a log2 scale

I hope this clarifies things :-)