Eliminate "all" for single chromosome assemblies

[jrobinso]

In the special case of single chromosome assemblies, there is no difference in "All" and the chromosome. So for this case make 2 changes

(1) add the whole-genome resolution to the list of explicitly specified ones
(2) eliminate "All" from the chromosome pulldown menu

[lidaof]

Hi @jrobinso , can I used 'all' in the 3rd parameter for straw API?
straw.getContactRecords(normalization,region1, 'all', units, binSize)?

tried, get a error with cannot getLength

[jrobinso]

That is not correct syntax. The region argument is an object with chr, start, and end.

[jrobinso]

The "all" query would not work even with correct syntax. I just pushed a fix for that, but the "region" arguments should look like this, do not specify start and end.

{
   chr: "ALL"
}

Also, do not specify a binSize, it is not relevant for "ALL". To use this you will need to pull and build (with grunt).

In the future please open a new issue for a new problem or question, this is not related to the original issue. It helps with tracking.

[jrobinso]

BTW the "all" chromosome is used only for display, it is not really useful or suitable for analysis. The units are kb (not bp), and original chromosome information is lost.

[lidaof]

Thanks @jrobinso . I was thinking it's kinda related so didn't open a new issue.
From what you said, suppose I should not use 'all' to get all the interactions (in genome) with one region?

Currently what I am doing is put all chrom object (with chr, start, end) in an array and loop it with my single query region to get all interactions. That;s why I was asking if I can use all instead of a for loop.

Thanks again.

[jrobinso]

It depends on what you are doing. If you are doing analysis I would not use "ALL", its is just used to get an approximate coarse scale view for visualization. You can't even know the bin size easily. If you want to paint a whole genome summary like juicebox does it is fine, but remember the coordinates are kilo-bases from the start of the first chromosome.

[lidaof]

@jrobinso Thank you so much for clarifying.