creating bed file for IGB

[Arnaud CEOL]

Hi,

I'm creating bed files to load mutation positions in IGB (version 8).

Let say I've a mutation on chromosome 1 position 1000 (this is a totally arbitrary position), I added the following line in the bed file:

chr1 1000 1000

But nothing apears in IGB.

After a few tests, I understood that the start and end position in the bed file should be different, so I created a new file with the row:
chr1 1000 1001

But I still have a doubt on whether it should be indeed
chr1 1000 1001

or

chr1 999 1000

Am I correct, and if yes which is the good solution?

thanks,

Arnaud

[Ann E. Loraine]

Hi Arnaud,

To indicate a SNP affecting the 1st base on chr1, you would say:

chr1 0 1

where 0 is the start of the SNP and 1 is the end of the SNP.

This is because BED is using interbase coordinates. IGB should draw this as a single block exactly one base wide.

Also, in bed format, end is always larger than start and the length of the feature is end - start, which is 1 in this case.

Here is a pretty good explanation of how interbase works:

http://bergmanlab.smith.man.ac.uk/?p=36

Also I want to let you know that we've moved the IGB code base to this new git repo:

https://bitbucket.org/lorainelab/integrated-genome-browser

We hope this will make it easier for you and other developers to make changes to the code base. All you'd have to do is fork the repo w/in bitbucket, make changes as needed, and then issue a pull request to get the changes incorporated into the master.

During the next week we'll update the Developer's Guide to describe the details. And of course please let us know if you have suggestions!

All the best,

Ann

[Arnaud CEOL]

Thank you very much!