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 . - . [email protected]@uc004dsz.2;[email protected] @uc004dsz.2;[email protected]@uc004dsz.2 chrX ALE mRNA 54094757 54099720 . - . [email protected]@uc004dsz.2.B;[email protected] @uc004dsz.2;[email protected]@uc004dsz.2.B;[email protected] @uc004dsz.2 chrX ALE exon 54094757 54099720 . - . [email protected]@uc004dsz.2.B.0;[email protected] @uc004dsz.2.B;[email protected]@uc004dsz.2.B.0;[email protected] @uc004dsz.2 chrX ALE mRNA 54200222 54200579 . - . [email protected]@uc004dsz.2.A;[email protected] @uc004dsz.2;[email protected]@uc004dsz.2.A;[email protected] @uc004dsz.2 chrX ALE exon 54200222 54200579 . - . [email protected]@uc004dsz.2.A.0;[email protected] @uc004dsz.2.A;[email protected]@uc004dsz.2.A.0;[email protected] @uc004dsz.2 paired end: [email protected]@uc004dsz.2 0.98 0.93 1.0 0.42 0.35 0.5 0.56 1000000000000.0 ('[email protected]@uc004dsz.2.B.0', '[email protected]@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: [email protected]@uc004dsz.2 1.00 1.00 1.00 0.94 0.93 0.95 0.06 1000000000000.00 '[email protected] @uc004dsz.2.B.0','[email protected]@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 . - . [email protected] @uc010mwh.1uc004bny.1uc004bnz.1;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1 chr9 ALE mRNA 126141933 126144904 . - . [email protected] @uc010mwh.1uc004bny.1uc004bnz.1.B;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1.B;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1 chr9 ALE exon 126141933 126144904 . - . [email protected] @uc010mwh.1uc004bny.1uc004bnz.1.B.0;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1.B;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1.B.0;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1 chr9 ALE mRNA 126163870 126164191 . - . [email protected] @uc010mwh.1uc004bny.1uc004bnz.1.A;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1.A;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1 chr9 ALE exon 126163870 126164191 . - . [email protected] @uc010mwh.1uc004bny.1uc004bnz.1.A.0;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1.A;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1.A.0;[email protected] @uc010mwh.1uc004bny.1uc004bnz.1 paired end: [email protected]@uc010mwh.1uc004bny.1uc004bnz.1 0.36 0.3 0.44 0.68 0.570.78 -0.32 12557315.78 ('[email protected]@uc010mwh.1uc004bny.1uc004bnz.1.B.0', '[email protected]@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: [email protected]@uc010mwh.1uc004bny.1uc004bnz.1 0.89 0.88 0.91 0.97 0.960.98 -0.08 1000000000000.00 '[email protected] @uc010mwh.1uc004bny.1uc004bnz.1.B.0','[email protected]@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
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