[miso-users] paired end vs. single end modes

Wed Sep 30 18:59:21 EDT 2015

Dear Yarden,

I have a question regarding paired end versus single end options. I have
paired end libraries and I use the annotation files that are provided in
Miso webpage.

As suggested in the documentation (possibility of missing events having
short length in paired end mode), I tried both single end and paired end
modes. I realized that single end mode could detect more events with a
descent overlap with paired end results (considering diff cutoff of 0.1 for
both options)

However, when I check the events that are detected in paired-end mode but
not in single end mode, I find that they have big bayes factors, but the
difference in PSIs is small. It mostly happens for regions where there is a
huge difference between isoform lengths (isoform1 vs. isoform2). Please
have a look at the two examples below:
--------------------------------------------------
Example 1:
annotation:
chrX    ALE    gene    54094757    54200579    .    -    .
ID=54954 at uc004dta.2@uc004dsz.2;Name=54954 at uc004dta.2
@uc004dsz.2;gid=54954 at uc004dta.2@uc004dsz.2
chrX    ALE    mRNA    54094757    54099720    .    -    .
ID=54954 at uc004dta.2@uc004dsz.2.B;Parent=54954 at uc004dta.2
@uc004dsz.2;Name=54954 at uc004dta.2@uc004dsz.2.B;gid=54954 at uc004dta.2
@uc004dsz.2
chrX    ALE    exon    54094757    54099720    .    -    .
ID=54954 at uc004dta.2@uc004dsz.2.B.0;Parent=54954 at uc004dta.2
@uc004dsz.2.B;Name=54954 at uc004dta.2@uc004dsz.2.B.0;gid=54954 at uc004dta.2
@uc004dsz.2
chrX    ALE    mRNA    54200222    54200579    .    -    .
ID=54954 at uc004dta.2@uc004dsz.2.A;Parent=54954 at uc004dta.2
@uc004dsz.2;Name=54954 at uc004dta.2@uc004dsz.2.A;gid=54954 at uc004dta.2
@uc004dsz.2
chrX    ALE    exon    54200222    54200579    .    -    .
ID=54954 at uc004dta.2@uc004dsz.2.A.0;Parent=54954 at uc004dta.2
@uc004dsz.2.A;Name=54954 at uc004dta.2@uc004dsz.2.A.0;gid=54954 at uc004dta.2
@uc004dsz.2

paired end:
54954 at uc004dta.2@uc004dsz.2    0.98    0.93    1.0    0.42    0.35
0.5    0.56    1000000000000.0    ('54954 at uc004dta.2@uc004dsz.2.B.0',
'54954 at uc004dta.2@uc004dsz.2.A.0')    (0,0):1063,(1,0):1494    0:1494
(0,0):603,(0,1):41,(1,0):855    0:855,1:41    chrX    NA    (54094757,
54200222)    (54099720, 54200579)

single end:
54954 at uc004dta.2@uc004dsz.2    1.00    1.00    1.00    0.94    0.93
0.95    0.06    1000000000000.00    '54954 at uc004dta.2
@uc004dsz.2.B.0','54954 at uc004dta.2@uc004dsz.2.A.0'
(0,0):2168,(0,1):6,(1,0):30720:3072,1:6
(0,0):1245,(0,1):109,(1,0):1746    0:1746,1:109    chrX    NA
54094757,54200222    54099720,54200579

----------------------------------------------
Example 2:
chr9    ALE    gene    126141933    126164191    .    -    .
ID=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1;Name=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1;gid=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1
chr9    ALE    mRNA    126141933    126144904    .    -    .
ID=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1.B;Parent=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1;Name=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1.B;gid=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1
chr9    ALE    exon    126141933    126144904    .    -    .
ID=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1.B.0;Parent=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1.B;Name=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1.B.0;gid=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1
chr9    ALE    mRNA    126163870    126164191    .    -    .
ID=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1.A;Parent=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1;Name=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1.A;gid=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1
chr9    ALE    exon    126163870    126164191    .    -    .
ID=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1.A.0;Parent=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1.A;Name=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1.A.0;gid=57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1

paired end:
57706 at uc004boa.1uc004bob.1@uc010mwh.1uc004bny.1uc004bnz.1    0.36    0.3
0.44    0.68    0.570.78    -0.32    12557315.78
('57706 at uc004boa.1uc004bob.1@uc010mwh.1uc004bny.1uc004bnz.1.B.0',
'57706 at uc004boa.1uc004bob.1@uc010mwh.1uc004bny.1uc004bnz.1.A.0')
(0,0):552,(0,1):49,(1,0):587    0:587,1:49
(0,0):275,(0,1):17,(1,0):770    0:770,1:17    chr9    NA    (126141933,
126163870)    (126144904, 126164191)

single end:
57706 at uc004boa.1uc004bob.1@uc010mwh.1uc004bny.1uc004bnz.1    0.89
0.88    0.91    0.97    0.960.98    -0.08    1000000000000.00
'57706 at uc004boa.1uc004bob.1
@uc010mwh.1uc004bny.1uc004bnz.1.B.0','57706 at uc004boa.1uc004bob.1@uc010mwh.1uc004bny.1uc004bnz.1.A.0'
(0,0):1119,(0,1):148,(1,0):1228
0:1228,1:148(0,0):523,(0,1):50,(1,0):1605    0:1605,1:50    chr9    NA
126141933,126163870    126144904,126164191
---------------------------------------------------

I am using Miso version 0.4.9. Could you please help me figure out why this
happens in single end mode?

Thanks,
Alborz
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.mit.edu/pipermail/miso-users/attachments/20150930/df60ee14/attachment.html