Question: Understanding MISO filtered events output
0
gravatar for priyankamaripuri
3.5 years ago by
india
priyankamaripuri40 wrote:

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.

Thanx in advance.

rna-seq • 800 views
ADD COMMENTlink written 3.5 years ago by priyankamaripuri40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1115 users visited in the last hour