ConstructBins

[deepti jain]

I am using the constructBins function of mosaics and I have two
questions:

1)I was wondering, what chromosome sizes and number constructBins uses
as it does seem to have any option for entering the organism/
assembly (eg:mm9)

2)Are the bin co-ordinates comparable between mutiple files?

Thanks.

[deepti jain]

Sorry, the first question in the last mail should be

1)I was wondering, what chromosome sizes and number constructBins
uses

as it does NOT seem to have any option for entering the organism/
assembly (eg:mm9)

Also, i have one more question:

Does construcBins shift reads? If yes,is this the reason it has the
fragment size option?

Thanks.

[Dongjun Chung]

Hi Deepti,

Thanks for your interest in our mosaics package.

> 1)I was wondering, what chromosome sizes and number constructBins uses
> as it does seem to have any option for entering the  organism/
> assembly (eg:mm9)
>

In the current implementation, the chromosome sizes and numbers are extracted from the aligned read files. Specifically, any chromosomes that more than one read aligned to are included in the bin-level files and the chromosome size is determined as the maximum of coordinates that reads aligned to within the chromosome.

I am thinking about incorporating options specifying list of chromosomes and their sizes in the next version of mosaics package.

> 2)Are the bin co-ordinates comparable between mutiple files?
>

Because of the strategies mentioned in (1), bin-level files with slightly different chromosome sizes could be constructed for different aligned read files.

Does construcBins shift reads? If yes,is this the reason it has the
fragment size option?

 
constructBins() "extends" reads to the fragment size, instead of shifting them.

Thanks,
Dongjun