Comments (7)
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.
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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 !
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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".
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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 ) ?
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Our reference allele is different from that in GRCH38.
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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 ) ?
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Please find the reference allele in the supplementary table of the manuscript.
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Related Issues (20)
- ExtractHLAread.sh HOT 5
- ExtractHLAread.sh syntax errors. HOT 4
- MICA and MICB HOT 3
- Identify somatic HLA mutation from SpecHLA HOT 6
- Performace among Novoalign V4, V3 and Bowtie2 in read-binning step HOT 2
- HLA typing only based on long-read RNA-seq data? HOT 2
- Feature request HOT 7
- Low confidence result for all HLA genes HOT 10
- Question about minimap2 parameters in long_read_typing.py HOT 15
- complaining about dependencies / empty output files HOT 7
- how to get hla_gen.format.filter.extend.DRB.no26789.fasta ? HOT 5
- Couldn't run a test on example files of exon. I saw this error related to libtinfo.so.5: version `NCURSES_TINFO_5.0.19991023' HOT 6
- Typing long reads HOT 7
- 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
- Bug report : Cannot find sample.realign.sort.bam for long read typing
- Got different allele result for different IMGT version
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