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<p class="MsoNormal"><span style="font-size:11.0pt">Folks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I have a question about MISO output and you folks are experts.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I have a dataset analyzed and now I am vetting the respective output.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">For a candidate gene with three transcripts, I see from the *bf file:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Sample1_counts S1_assigned_counts Sample1_counts
S2_assigned_counts<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">(0,0,0):3117,(0,0,1):19,(0,1,0):543,(1,0,0):2,(1,0,1):303,(1,1,1):135<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">0:261,1:639,2:102<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">(0,0,0):3049,(0,0,1):21,(0,1,0):640,(1,0,0):2,(1,0,1):241,(1,1,1):127<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">0:195,1:734,2:102<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">The assigned_counts per transcript seem to make sense
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">However, for the assigned counts, the largest numbers are seen for the “(0,0,0): 3117” and “(0,0,0): 3049” cases.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">From the on-line manual<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">“The field (0,0):N, if outputted, indicates the number of reads N that mapped to the region but were thrown out (e.g. because they are not consistent with the isoforms in the annotation, violate overhang constraints,
or other related reasons.)”<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">1) Have you seen this before?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">2) How can I evaluate whether or not that result is correct? That is, am I really throwing out 3K reads per the manual? Remember this is for a single event/Gene. If so I am losing a lot of data.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">3) How do you handle replicates? Miso works on pairs.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Cheers, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Starr <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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