search

jonathonthill / MMAPPR2

Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
4 stars 3 forks source link

How to run loess when there are large gaps in a chromosome? #104

Open xiekunwhy opened 4 years ago

xiekunwhy commented 4 years ago

Hi,

In some(or many when genome size is large) cases, loess always stop abnormally because there are some big gaps between snp markers, any tips to deal with this problem?

Best, Kun

jonathonthill commented 4 years ago

Hi Kun,

I am afraid this software is not quite ready for use yet. We are still working on some bugs and testing it as thoroughly as we can. Do you have a file you could send? We could then include it in our testing.

xiekunwhy commented 4 years ago

Hi @jonathonthill

Here are some ed results from a common wheat bsr project, and marker density is very low, large gap can always crashing loess function.

bsr.ed.txt

Best, Kun

jonathonthill commented 4 years ago

Hi Kun,

Is there any way to get me the aligned files and reference?

Thanks,

Jonathon

On Jul 22, 2020, at 8:59 PM, xiekunwhy notifications@github.com wrote:

Hi @jonathonthill https://github.com/jonathonthill Here are some ed results from a common wheat bsr project, and marker density is very low, large gap can always crashing loess function.

bsr.ed.txt https://github.com/kjohnsen/MMAPPR2/files/4963642/bsr.ed.txt Best, Kun

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/kjohnsen/MMAPPR2/issues/104#issuecomment-662795632, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSNKBPZ2N3CQD6TLOYNAJDR46RPTANCNFSM4PCBIT6Q.