[miso-users] variable length reads

[Gábor Csárdi]

Michael,

there was no progress on this I'm afraid. At least nothing more than
adding an issue for it:
https://github.com/yarden/MISO/issues/12

I am planning to do this, quite soon. It is not very difficult to
implement, the only problematic thing is that the current MISO sampler
implementation heavily uses the fact that all reads have the same
length, for optimization.
Adding variable read lengths basically means writing another (slightly
slower) version of the sampler, that does not rely on the constant
read length.

Thanks for offering the help. I am currently heavily reworking the
sampler, to add automatic convergence detection. (The default constant
number of iterations works well for most genes, but sometimes does not
converge for genes with many isoforms.) I am doing this in the
'fastmiso' branch, the single-end version is finished, although needs
some testing, and I am writing the paired-end version. Once this is
done, I'll do the variable read length stuff, probably sometime next
week.

Best,
Gabor

On Wed, Sep 28, 2011 at 3:41 PM, Michael Lovci <michaeltlovci at gmail.com> wrote:
> Has anyone made any progress updating miso to include reads outside of the
> length set by --read-len ? What are the particular problems with
> implementing this?  Can I be of any help in writing this part?
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-- 
Gabor Csardi <gcsardi at stat.harvard.edu>  Dpt of Statistics, Harvard University