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2 Questions about model 2 and python/c++ preprocess #35
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Hi Pan,
thanks for your email
On Wed, 6 Mar 2024 at 21:35, panagi0tis90 ***@***.***> wrote:
Dear authors,
Thank you for the useful software. I am facing 2 "problems", so i was
thinking if you could help me. My 2 questions are:
1. I installed a conda env and i performed analysis on the test data
you provided to see if all is ok. Although with python_proprocess script
the output values were identical with the ones provided, when i run c++
proprocess choice, the probabilities are entirely different (in both model1
and 2). Is there an explanation to this? Maybe i use a different c++
version or something like that?
Are all probabilities different or just some of them?
The C++ preprocessing script rescues additional signals in boundary sites
(near the edge of reads or next of unaligned deletions), so I would only
expect some of the probabilities to be different
1. I run an experiment of 1.3m reads. Initially, i run model2 with
default parameters. When i changed the minimum reads to n=10 (i would like
to get extra points because in minION many genes are around 10 reads), i
got a lot of notifications "Warning: Stoichiometry cannot compute, try less
stringent double cutoff values". Is this something to worry about? With
default parameters i hardly get any notification like this. Eventually i
got more points, but still i dont know if there is something wrong with
this.
Stoichiometry is estimated from the individual reads aligned to a site,
using reads that have P>0.7 (modified) or P<0.3 (non-modified). So reducing
the number of reads to 10 may result in running out of available reads for
the stoichiometry estimate.
Two possibilities could be
1) modified the double threshold, e.g. (0.3,0.7)->(0.5,0.5)
2) work with the individual reads from those sites and assess the sites
using the individual read data directly.
I hope this helps
Best
Eduardo
…
Thanks in advance!!
Pan
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Dear authors,
Thank you for the useful software. I am facing 2 "problems", so i was thinking if you could help me. My 2 questions are:
Thanks in advance!!
Pan
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