Comments (5)
Hi, to reduce computational resources, we only keep one allele at the 2-field resolution in the read binning step.
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Hi, to reduce computational resources, we only keep one allele at the 2-field resolution in the read binning step.
thank you for your reply ! could you send me some scripts to build this fasta reference ?
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The script to generate the reference is not kept. You can just retain one allele for each group of alleles with the same two-field type. Also, you can simply keep all the alleles.
from spechla.
The script to generate the reference is not kept. You can just retain one allele for each group of alleles with the same two-field type. Also, you can simply keep all the alleles.
Hello,
I find this file hla_gen.format.filter.extend.DRB.no26789.fasta don't update its allele list against IMGT3.39 .
for example,
the next list is in hla_gen.format.filter.extend.DRB.no26789.fasta .
DQB102:01
DQB102:02
DQB103:01
DQB103:02
DQB103:04
DQB103:05
DQB103:19
DQB104:01
DQB104:02
DQB105:01
DQB105:02
DQB105:03
DQB105:04
DQB106:01
DQB106:02
DQB106:03
DQB106:04
DQB106:07
DQB106:08
DQB106:09
DQB106:10
DQB106:11
DQB106:14
DQB106:20
but I check DQB1 in IMGTHLA-3.39.0-alpha/fasta/DQB1_gen.fasta and find so many alleles not in that file .
for example, these below alleles not in hla_gen.format.filter.extend.DRB.no26789.fasta.
HLA:HLA06518 DQB106:44 6373 bp
HLA:HLA06877 DQB106:46 6700 bp
HLA:HLA07539 DQB106:48:01 6561 bp
HLA:HLA07820 DQB106:49 6671 bp
HLA:HLA09472 DQB106:84 7102 bp
HLA:HLA09733 DQB106:90 7103 bp
this situation will cause that specHLA miss some allele typing ?
Expecting your reply !
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Please have a look at the manuscript for this part.
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Related Issues (20)
- ExtractHLAread.sh HOT 5
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- Index command fails but reports success HOT 1
- how to assign read to gene ? HOT 1
- use deep-variants calling too to replace longshot ? HOT 1
- Reason for setting bias value for annoHLA.pl
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