hla database updata #1
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You may want to inspect the msa files, especially toward the end of the
alignment, and manually delete the sequences that extend beyond the
alignment blocks. good luck!
…On Fri, Apr 8, 2022 at 12:59 AM shiwanyin ***@***.***> wrote:
Hi,cliu32
After i updata hla database to 3.46, I met an error "err: process_block:
block size != refs size" when i use athlates typing function. I try some
times and still get this error.
could you give me some advices ?
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Thanks for your apply. I still feel confused about the 'alignment blocks'. |
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The IMGT MSA format is not standard, for example, the file for A may look
like the following. The last line is due to a frameshift and is not part of
any alignment. You may delete the last few lines and try again. Other loci
may be affected as well and need manual editing. Good luck.
...
A*80:04 --- --- --- --- --- --- --- --- --- -|-- ---
A*80:05 --- --- --- --- --- --- --- --- --- -|-- ---
A*80:06 --- --- --- --- --- --- --- --- --- -|-- ---
A*80:07 --- --- --- --- --- --- --- --- --- -|-- ---
A*80:08N --- --- --- --- --- --- --- --- --- -|-- ---
A*80:09N *** *** *** *** *** *** *** *** *** *|** ***
cDNA 1098
AA codon 342
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A*03:437Q GACAG CTGCC TTGTG TGGGA CTGA
…On Thu, Apr 14, 2022 at 2:48 AM shiwanyin ***@***.***> wrote:
Thanks for your apply. I still feel confused about the 'alignment blocks'.
I directly get the msa file from imgt hla database without any change. i
use your code to get ref and bed files and the the input of your code is
simply the combine of gDNA fasta and cDNA fasta.
what i confused is that i do not know what is the 'alignment block' does
your mean.
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which locus? did you edit all msa files affected by the non-standard
formatting?
sorry to hear about the trouble. in the worst-case scenario, I don't think
you need to update the database if this is for research only.
…On Tue, May 10, 2022 at 3:06 AM shiwanyin ***@***.***> wrote:
The IMGT MSA format is not standard, for example, the file for A may look
like the following. The last line is due to a frameshift and is not part of
any alignment. You may delete the last few lines and try again. Other loci
may be affected as well and need manual editing. Good luck. ... A*80:04
--- --- --- --- --- --- --- --- --- -|-- --- A*80:05 --- --- --- --- ---
--- --- --- --- -|-- --- A*80:06 --- --- --- --- --- --- --- --- --- -|--
--- A*80:07 --- --- --- --- --- --- --- --- --- -|-- --- A*80:08N --- ---
--- --- --- --- --- --- --- -|-- --- A*80:09N *** *** *** *** *** *** ***
*** *** *|** *** cDNA 1098 AA codon 342 | A
*03:437Q GACAG CTGCC TTGTG TGGGA CTGA … <#m_6298155279951270454_> On Thu,
Apr 14, 2022 at 2:48 AM shiwanyin @.**> wrote: Thanks for your apply. I
still feel confused about the 'alignment blocks'. I directly get the msa
file from imgt hla database without any change. i use your code to get ref
and bed files and the the input of your code is simply the combine of gDNA
fasta and cDNA fasta. what i confused is that i do not know what is the
'alignment block' does your mean. — Reply to this email directly, view it
on GitHub <#1 (comment)
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thanks ! i edit my MSA file with your solution, it works on IMGT/HLA 3.29
release. but it still get the same error when i use the latest release
IMGT/HLA database.
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yes, i removed all msa files affected by frameshift that appeared at the end of msa file. I guess there are other not-standard formats in the latest msa files. But I can not figure out them. well, I not only use it for research but for clinical in some situation |
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Thanks for your apply. I still feel confused about the 'alignment blocks'.
I directly get the msa file from imgt hla database without any change. i use your code to get ref and bed files and the the input of your code is simply the combine of gDNA fasta and cDNA fasta.
what i confused is that i do not know what is the 'alignment block' does your mean.
At 2022-04-09 21:03:01, "Chang Liu" ***@***.***> wrote:
You may want to inspect the msa files, especially toward the end of the
alignment, and manually delete the sequences that extend beyond the
alignment blocks. good luck!
On Fri, Apr 8, 2022 at 12:59 AM shiwanyin ***@***.***> wrote:
Hi,cliu32
After i updata hla database to 3.46, I met an error "err: process_block:
block size != refs size" when i use athlates typing function. I try some
times and still get this error.
could you give me some advices ?
—
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[image: image.png]
Attached is an example for HLA-C nuc alignment. Three alleles have extended
transcripts due to frameshift, which are outside of the standard alignment
blocks above.
Try deleting the extra sequence and see what happens. Good luck.
…On Tue, Oct 11, 2022 at 3:47 AM shiwanyin ***@***.***> wrote:
Thanks for your apply. I still feel confused about the 'alignment blocks'.
I directly get the msa file from imgt hla database without any change. i
use your code to get ref and bed files and the the input of your code is
simply the combine of gDNA fasta and cDNA fasta.
what i confused is that i do not know what is the 'alignment block' does
your mean.
At 2022-04-09 21:03:01, "Chang Liu" ***@***.***> wrote:
You may want to inspect the msa files, especially toward the end of the
alignment, and manually delete the sequences that extend beyond the
alignment blocks. good luck!
On Fri, Apr 8, 2022 at 12:59 AM shiwanyin ***@***.***> wrote:
> Hi,cliu32
> After i updata hla database to 3.46, I met an error "err: process_block:
> block size != refs size" when i use athlates typing function. I try some
> times and still get this error.
> could you give me some advices ?
>
> —
> Reply to this email directly, view it on GitHub
> <#1>, or unsubscribe
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https://github.com/notifications/unsubscribe-auth/ACOAQWOCNQAALERAHQTDEZTVD7DLDANCNFSM5S3PK5IA
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Hi,cliu32
After i updata hla database to 3.46, I met an error "err: process_block: block size != refs size" when i use athlates typing function. I try some times and still get this error.
could you give me some advices ?
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