what's the meanning of "interval_dict" in long_read_typing.py ?

[lidd77]

Hello , professor,
For "A":"HLA_A:1000-4503" from the below code line , what's the meaning for these two number "1000" and "4503" ?
and how to get these coordinate number values ,like "C:1000-5304", "DPA1:1000-10775" ?
'''
interval_dict = {"A":"HLA_A:1000-4503", "B":"HLA_B:1000-5081","C": "HLA_C:1000-5304","DPA1":"HLA_DPA1:1000-10775",
"DPB1":"HLA_DPB1:1000-12468","DQA1":"HLA_DQA1:1000-7492","DQB1":"HLA_DQB1:1000-8480","DRB1":"HLA_DRB1:1000-12229" }
'''

Expecting your reply !

thank you .

[wshuai294]

Hello, because we added upstream and downstream extended 1000bp sequences to the reference allele. So the interval like "C:1000-5304" represents the actual gene sequence intervals.

[lidd77]

Hello, because we added upstream and downstream extended 1000bp sequences to the reference allele. So the interval like "C:1000-5304" represents the actual gene sequence intervals.

sorry , could you give us a script to show us how to get the interval , for example , how to get the interval for HLA-A ?
I know HLA-A 's GRCH38 position is chr6:29,941,260-29,949,572, so how to get the interval ?
I want to know exactly how to set the interval so that I can understand specHLA deeply and modify and test this interval effect.

Expecting your reply !

[wshuai294]

Hello. For example, we extract the upstream sequence of chr6:29,940,260-29,941,260 (left seq), and the downstream sequence of chr6:29,949,572-29,949,572 (right seq). After that, we combine these two sequences and our reference allele (left seq + allele + right seq). In this case, the edited ref's length is 5503. And the actual HLA-A sequence is in HLA_A:1000-4503".

[lidd77]

Hello. For example, we extract the upstream sequence of chr6:29,940,260-29,941,260 (left seq), and the downstream sequence of chr6:29,949,572-29,949,572 (right seq). After that, we combine these two sequences and our reference allele (left seq + allele + right seq). In this case, the edited ref's length is 5503. And the actual HLA-A sequence is in HLA_A:1000-4503".

it is typo error ? for downstream sequence is chr6:29,949,572-(29,949,572+4503 ) ?

[wshuai294]

Our reference allele is different from that in GRCH38.

[lidd77]

it is typo error ? for downstream sequence is chr6:29,949,572-(29,949,572+4503 ) ?

for downstream sequence is chr6:29,949,572-(29,949,572+1000 ) ?

[wshuai294]

Please find the reference allele in the supplementary table of the manuscript.