[miso-users] Assigning (1,1) reads in MISO

[Jake Yeung]

Hi all,

This is my first post, sorry if it sounds too naive. I have read the 
paper and the supplementary, but I still have some trouble understanding 
the way sample_counts in (1,1) go to sample_assigned.

For example, for finding the PSI values for SE events in a particular 
sample, I have the following outputs for three events:
event=> 
chr2:238427182:238427291:+ at chr2:238428553:238428672:+ at chr2:238434244:238434448:+
counts => (0,0):1028,(0,1):10,(1,0):422,(1,1):462
assigned_counts=> 0:756,1:138
*334 (1,1) counts assigned to first isoform, 128 (1,1) counts assigned 
to second isoform.*

event=>chr2:70520750:70520869:- at chr2:70516482:70516504:- at chr2:70515200:70515324:-
counts=>(0,0):126,(0,1):4,(1,0):54,(1,1):186
assigned_counts=>0:207,1:37
*153 (1,1) counts assigned to first isoform, 33 (1,1) counts assigned to 
second isoform.*

event=>chr2:122513236:122513529:+ at chr2:122514816:122515010:+ at chr2:122516286:122516382:+
counts=>(0,0):46,(1,0):5,(1,1):27
assigned_counts=>0:8,1:24
*3 (1,1) counts assigned to first isoform, 24 (1,1) counts assigned to 
second isoform. *

I realize there may be a large number of factors that may affect the way 
(1,1) counts are assigned but I am a bit confused as to why for the last 
event, why 24 (1,1) counts were assigned to second isoform when there 
was no evidence for (0,1) counts in that event.

Any help with insights with factors that affect the way (1,1) counts are 
assigned would be most appreciated. Thank you in advance.

Regards,


J
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