[miso-users] variable length reads

[Sean O'Keeffe]

Hi,
So if I have a BAM file of variable length reads averaging 25bps across the
file, can I set --read-len 25? or does MISO only work with fixed length
reads?

Thanks,
Sean.

On 29 September 2011 11:51, Gábor Csárdi <gcsardi at stat.harvard.edu> wrote:

> 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
>
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>
>
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