Entering edit mode
8.6 years ago
priyankamaripuri
▴
40
Hello,
I'm working with RNA-seq data and currently using MISO (Mixture-of-Isoforms) to quantify expression level of alternatively spliced genes.However, I'm having trouble understanding the filtered events file generated by it. Please help me with this.
Here are some generated from each AS Event:
A3 Event:
chr6:26411783:26411809:+@chr6:26412640|26413397:26415444:+ 0.75 0.7 0.8 0.38 0.09 0.63 0.37 16.74 ('chr6:26411783:26411809:+@chr6:26412640|26413397:26415444:+.A.up_chr6:26411783:26411809:+@chr6:26412640|26413397:26415444:+.A.coreAndExt', 'chr6:26411783:26411809:+@chr6:26412640|26413397:26415444:+.B.up_chr6:26411783:26411809:+@chr6:26412640|26413397:26415444:+.B.core') (0,0):118,(0,1):89,(1,0):13,(1,1):774 0:588,1:288 (0,0):6,(0,1):20,(1,0):1,(1,1):71 0:30,1:62 chr6 + (26411783, 26411783) (26415444, 26415444)
A5 Event:
chr6:34393902:34393573|34393805:-@chr6:34392849:34392998:- 0.27 0.17 0.44 0.74 0.57 0.91 -0.47 801.69 ('chr6:34393902:34393573|34393805:-@chr6:34392849:34392998:-.A.dn_chr6:34393902:34393573|34393805:-@chr6:34392849:34392998:-.A.coreAndExt', 'chr6:34393902:34393573|34393805:-@chr6:34392849:34392998:-.B.dn_chr6:34393902:34393573|34393805:-@chr6:34392849:34392998:-.B.core') (0,0):1493,(1,0):44,(1,1):33 0:53,1:24 (0,0):2459,(0,1):3,(1,0):100,(1,1):9 0:104,1:8 chr6 - (34392849, 34392849) (34393902, 34393902)
MXE Event:
chr6:112024088:112024237:-@chr6:112021307:112021471:-@chr6:112020718:112020873:-@chr6:112017480:112017659:- 0.08 0.06 0.11 0.53 0.43 0.63 -0.45 1000000000000.0 ('chr6:112024088:112024237:-@chr6:112021307:112021471:-@chr6:112020718:112020873:-@chr6:112017480:112017659:-.A.dn_chr6:112024088:112024237:-@chr6:112021307:112021471:-@chr6:112020718:112020873:-@chr6:112017480:112017659:-.A.mxe1_chr6:112024088:112024237:-@chr6:112021307:112021471:-@chr6:112020718:112020873:-@chr6:112017480:112017659:-.A.up', 'chr6:112024088:112024237:-@chr6:112021307:112021471:-@chr6:112020718:112020873:-@chr6:112017480:112017659:-.B.dn_chr6:112024088:112024237:-@chr6:112021307:112021471:-@chr6:112020718:112020873:-@chr6:112017480:112017659:-.B.mxe2_chr6:112024088:112024237:-@chr6:112021307:112021471:-@chr6:112020718:112020873:-@chr6:112017480:112017659:-.B.up') (0,0):1131,(0,1):470,(1,0):43,(1,1):37 0:46,1:504 (0,0):130,(0,1):46,(1,0):54,(1,1):7 0:59,1:48 chr6 - (112017480, 112017480) (112024237, 112024237)
RI Event:
chr6:33386065-33385646:-@chr6:33385472-33385258:- 0.91 0.8 0.98 0.65 0.6 0.7 0.26 27.11 ('chr6:33386065-33385646:-@chr6:33385472-33385258:-.A.withRI', 'chr6:33386065-33385646:-@chr6:33385472-33385258:-.B.dn_chr6:33386065-33385646:-@chr6:33385472-33385258:-.B.up') (0,0):6,(0,1):2,(1,0):52,(1,1):2 0:54,1:2 (0,0):423,(0,1):113,(1,0):298,(1,1):16 0:310,1:117 chr6 - (33385258, 33385258) (33386065, 33386065)
SE Event:
chr6:43746626:43746655:+@chr6:43749693:43749789:+@chr6:43752278:43754223:+ 0.1 0.03 0.22 0.45 0.27 0.68 -0.35 90.22 ('chr6:43746626:43746655:+@chr6:43749693:43749789:+@chr6:43752278:43754223:+.A.up_chr6:43746626:43746655:+@chr6:43749693:43749789:+@chr6:43752278:43754223:+.A.se_chr6:43746626:43746655:+@chr6:43749693:43749789:+@chr6:43752278:43754223:+.A.dn', 'chr6:43746626:43746655:+@chr6:43749693:43749789:+@chr6:43752278:43754223:+.B.up_chr6:43746626:43746655:+@chr6:43749693:43749789:+@chr6:43752278:43754223:+.B.dn') (0,0):95,(0,1):14,(1,0):3,(1,1):438 0:79,1:376 (0,0):312,(0,1):3,(1,0):10,(1,1):306 0:125,1:194 chr6 + (43746626, 43746626) (43754223, 43754223)
The main challenge I have been facing is in understanding the event name and the isoforms.
Thanks in advance.
