Folks,
I have a question about MISO output and you folks are experts.
I have a dataset analyzed and now I am vetting the respective output.
For a candidate gene with three transcripts, I see from the *bf file:
Sample1_counts
S1_assigned_counts
Sample1_counts
S2_assigned_counts
(0,0,0):3117,(0,0,1):19,(0,1,0):543,(1,0,0):2,(1,0,1):303,(1,1,1):135
0:261,1:639,2:102
(0,0,0):3049,(0,0,1):21,(0,1,0):640,(1,0,0):2,(1,0,1):241,(1,1,1):127
0:195,1:734,2:102
The assigned_counts per transcript seem to make sense
However, for the assigned counts, the largest numbers are seen for the
“(0,0,0): 3117” and “(0,0,0): 3049” cases.
From the on-line manual
“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.)”
1) Have you seen this before?
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.
3) How do you handle replicates? Miso works on pairs.
Cheers,
Starr
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