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<DIV>Hi, colleague:</DIV>
<DIV> </DIV>
<DIV>I have several questions:</DIV>
<DIV>1. In your 2008 Nature paper,the
'inclusion ratio' is defined as the ratio of the number of 'inclusion¡¯ reads to inclusion plus ¡®exclusion¡¯ reads.</DIV>
<DIV>Are the reads used here those assigned by MISO using Bayesian
method? </DIV>
<DIV> </DIV>
<DIV>2. When calculating PSI, the density of reads were used
(reads per position), i.e. one need to divide the above
(assigned) reads with some length.</DIV>
<DIV>However, I have not found the definition of the effective
length in the paper. In the supplementary file, it was noted that
28nt were kept from both</DIV>
<DIV>sides of a junction (cause your original read is 32bp, thus can assure at
least 4bp overlapping the next exon). So in my understanding, the
effective</DIV>
<DIV>length of a junction is 28+28 (this could be changed to real read
length minus 4 ), while for event including a middle exon,
the length should be 28+28+length of included exon. Am I right? </DIV>
<DIV>And for A5SS or A3SS events, as there are reads spanning the boundary of
two events, how do you deal with them?</DIV>
<DIV> </DIV>
<DIV>3. Currently I am analyzing a set of pair-end RNA-sequencing data. The
insertion size is about 150nt but the read length is 101, so two reads
overlap.</DIV>
<DIV>When using MISO with pair-end mode, it showed low read coverage for many
events. Is MISO vulnerable for such condition?</DIV>
<DIV> </DIV>
<DIV>4. And the last question. In my result of TandemUTR analysis, it
is seen that the assigned read are greatly different between events, but
the PSIs are </DIV>
<DIV>similar (see below), is this normal?</DIV>
<DIV> </DIV>
<DIV>
<DIV>event_name miso_posterior_mean ci_low ci_high isoforms counts assigned_counts chrom strand mRNA_starts mRNA_ends</DIV>
<DIV>2d 0.28,0.26,0.27,0.20 0.24,0.22,0.25,0.18 0.31,0.31,0.33,0.22 '2d.1.0','2d.2.0','2d.3.0','2d.4.0' (0,0,0,0):1163,(0,0,0,1):6,(0,0,1,0</DIV>
<DIV>):1,(1,0,0,0):203 0:203,1:0,2:1,3:6 chr3 + 126545676,126543284,126518921,126303617 126546040,126543378,126521721,126304424</DIV> </DIV>
<DIV>Thanks.</DIV>
<DIV> </DIV>
<DIV>Peng </DIV>
<DIV> </DIV>
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