[miso-users] variable length reads

[Michael Lovci]

Only 25nt reads are used in the analysis, other reads are discarded.

http://genes.mit.edu/burgelab/miso/docs/#frequently-asked-questions

On Thu, Sep 29, 2011 at 11:31 AM, Sean O'Keeffe <so2346 at columbia.edu> wrote:

> 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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>> > miso-users at mit.edu
>> > http://mailman.mit.edu/mailman/listinfo/miso-users
>> >
>> >
>>
>>
>>
>> --
>> Gabor Csardi <gcsardi at stat.harvard.edu>  Dpt of Statistics, Harvard
>> University
>>
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>>
>>
>
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