Confusing about definition of chromosome

[Jingu Lee]

Hi Tobias,

I have a question about definition of chromosome.

In DELLY paper, 

......

"‘Translocations’ are detected as paired-ends mapping to different chromosomes.

  Four possible types of translocations are differentiated, whether the two chromosomes are in sorted order and whether the two chromosomes are inverted relative to each other."

......

I can't understand these sentences. 

"chromosomes are in sorted order" & "the two chromosomes are inverted relative to each other"

How do chromosomes have order? and How do chromosomes are inverted?

Thank you for reading my question.

[Tobias Rausch]

Please see my reply to Lauren. If you have 2 double-strand breaks on two different chromosomes the ends can be joined 3' to 5', 5' to 3', 3' to 3' or 5' to 5'. Delly writes the specific connection type of the translocation in the INFO:CT field.

-Tobias

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[Jingu Lee]

Hi, Tobias.

First of all, I'm sorry that I posted a question before checking this google group's board message.

I got lots of help from your reply so thanks you.

So, I would want whether my conclusion is correct or not.

When I integrated the result between the contents of paper and your reply,  the qualification for detecting translocation is only inter-chromosomal.(because translocation includes all cases;3'to5', 5'to3', 3'to3', 5'to5')

Is this conclusion right?

I always feel grateful for your help.

Thanks a lot.

[Tobias Rausch]

Yes, all translocations are inter-chromosomal. The intra-chromosomal rearrangements are part of the inversion-type, deletion-type and tandem-duplication type rearrangement calls of Delly.

-Tobias

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