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DaehwanKimLab / hisat-genotype

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Different NA12892 HLA results from tutorial #85

Open Tesson98 opened 4 hours ago

Tesson98 commented 4 hours ago

Hi @chbe-helix，

I hope this find you well. When trying to repeat the tutorial HLA typing results with ILMN/NA12892 sample, I got the outputfile named "assembly_graph-hla.NA12892_extracted_1_fq_gz-hla-extracted-1_fq.report" and the output was as follows, which was diffrent from tutorials (https://daehwankimlab.github.io/hisat-genotype/tutorials/#interpreting-output) but the same as results mentioned in issues #11:

`

    # VERSIONS:
    # HISAT2 - 2.2.1
    # HISAT-genotype - 1.3.2
    # Database - Database /dssg/home/acct-medzwli/medzwli/Tesson_main/Softwares/hisatgenotype/indicies/hla derived from HISATgenotype DB version: NONE
    # COMMAND:/dssg/home/acct-medzwli/medzwli/Tesson_main/Softwares/hisatgenotype/hisatgenotype --base hla --locus-list A -1 ILMN/NA12892.extracted.1.fq.gz -2 ILMN/NA12892.extracted.2.fq.gz --threads 16

    hisat2 graph
        1496 reads and 769 pairs are aligned
            1 A*02:01:01:01 (count: 419)
            2 A*02:251 (count: 407)
            3 A*02:610:02 (count: 405)
            4 A*02:524:02 (count: 403)
            5 A*02:650 (count: 403)
            6 A*02:01:123 (count: 402)
            7 A*02:647 (count: 401)
            8 A*02:01:126 (count: 400)
            9 A*02:562 (count: 400)
            10 A*02:645 (count: 400)

            1 ranked A*02:01:01:01 (abundance: 51.95%)
            2 ranked A*11:01:01:01 (abundance: 48.05%)

`

Was my output correct?

Thank you so much!

Tesson, 2024.10.19

Tesson98 commented 4 hours ago

Additional, If I tried to do MHC-I and MHC-II genotyping with ILMN/NA12892 sample, I got 100% abudance in DQB1 and DRB1 allele genes. For those genes, should I directly treated them as homozygous? For example, if I get "1 ranked DRB101:01:01 (abundance: 100.00%)" and "1 ranked DQB105:01:01:03 (abundance: 100.00%)", the DRB1 and DQB1 genotypes of this sample were DRB101:01:01-DRB101:01:01 and DQB105:01:01:03-DQB105:01:01:03 ? The output was as follows: `

    # VERSIONS:
     # HISAT2 - 2.2.1
     # HISAT-genotype - 1.3.2
     # Database - Database /dssg/home/acct-medzwli/medzwli/Tesson_main/Softwares/hisatgenotype/indicies/hla derived from HISATgenotype DB version: NONE
     # COMMAND:/dssg/home/acct-medzwli/medzwli/Tesson_main/Softwares/hisatgenotype/hisatgenotype --base hla -v --locus-list A,B,C,DPA1,DPB1,DPB2,DQA1,DQB1,DRA,DRB1,DRB5 -1 ILMN/NA12892.extracted.1.fq.gz -2 ILMN/NA12892.extracted.2.fq.gz --out-dir out

    hisat2 graph
        4377 reads and 2247 pairs are aligned
            1 DPA1*01:03:01:03 (count: 1556)
            2 DPA1*01:03:01:02 (count: 1536)
            3 DPA1*02:01:01:02 (count: 1497)
            4 DPA1*01:03:01:04 (count: 1482)
            5 DPA1*02:01:01:01 (count: 1438)
            6 DPA1*02:01:08 (count: 1395)
            7 DPA1*01:03:01:05 (count: 1386)
            8 DPA1*02:01:02 (count: 1372)
            9 DPA1*01:03:01:01 (count: 1337)
            10 DPA1*01:03:05 (count: 1320)

            1 ranked DPA1*02:01:01:02 (abundance: 52.97%)
            2 ranked DPA1*01:03:01:01 (abundance: 34.00%)
            3 ranked DPA1*02:01:01:01 (abundance: 7.80%)
            4 ranked DPA1*01:03:01:03 (abundance: 5.24%)
        5901 reads and 2987 pairs are aligned
            1 DPB1*03:01:01 (count: 2654)
            2 DPB1*45:01 (count: 2599)
            3 DPB1*104:01 (count: 2177)
            4 DPB1*16:01:01 (count: 2139)
            5 DPB1*463:01 (count: 2120)
            6 DPB1*584:01 (count: 1676)
            7 DPB1*40:01 (count: 1100)
            8 DPB1*398:01 (count: 889)
            9 DPB1*04:01:31 (count: 878)
            10 DPB1*04:01:01:01 (count: 877)

            1 ranked DPB1*06:01:01 (abundance: 50.56%)
            2 ranked DPB1*14:01:01 (abundance: 49.44%)
        9389 reads and 4743 pairs are aligned
            1 DPB2*01:01:01 (count: 3670)
            2 DPB2*03:01:01:03 (count: 2878)
            3 DPB2*02:01 (count: 2578)
            4 DPB2*03:01:01:01 (count: 2266)
            5 DPB2*03:01:01:02 (count: 2238)
            6 DPB2*01:01:02 (count: 1970)

            1 ranked DPB2*01:01:01 (abundance: 69.06%)
            2 ranked DPB2*01:01:02 (abundance: 22.72%)
            3 ranked DPB2*03:01:01:01 (abundance: 4.50%)
            4 ranked DPB2*03:01:01:02 (abundance: 3.72%)
        3313 reads and 1681 pairs are aligned
            1 DQA1*01:01:02 (count: 1458)
            2 DQA1*01:01:01:03 (count: 1432)
            3 DQA1*01:01:01:01 (count: 1401)
            4 DQA1*01:01:01:02 (count: 1390)
            5 DQA1*01:05:01 (count: 743)
            6 DQA1*01:04:01:02 (count: 729)
            7 DQA1*01:04:01:01 (count: 728)
            8 DQA1*01:04:01:04 (count: 665)
            9 DQA1*01:07Q (count: 664)
            10 DQA1*01:04:01:03 (count: 654)

            1 ranked DQA1*01:01:01:03 (abundance: 76.27%)
            2 ranked DQA1*01:01:01:01 (abundance: 23.73%)
        3547 reads and 1795 pairs are aligned
            1 DQB1*05:01:01:03 (count: 1795)
            2 DQB1*05:103 (count: 1748)
            3 DQB1*05:01:01:02 (count: 1746)
            4 DQB1*05:104 (count: 1744)
            5 DQB1*05:01:01:01 (count: 1681)
            6 DQB1*05:52 (count: 1027)
            7 DQB1*05:02:01 (count: 1010)
            8 DQB1*05:97 (count: 1010)
            9 DQB1*05:03:01:01 (count: 1009)
            10 DQB1*05:106 (count: 996)

            1 ranked DQB1*05:01:01:03 (abundance: 100.00%)
        3048 reads and 1532 pairs are aligned
            1 DRA*01:01:02 (count: 1007)
            2 DRA*01:02:01 (count: 904)
            3 DRA*01:02:02 (count: 886)
            4 DRA*01:01:01:02 (count: 802)
            5 DRA*01:01:01:03 (count: 790)
            6 DRA*01:01:01:01 (count: 742)
            7 DRA*01:02:03 (count: 616)

            1 ranked DRA*01:02:01 (abundance: 69.11%)
            2 ranked DRA*01:01:02 (abundance: 30.89%)
        5514 reads and 2794 pairs are aligned
            1 DRB1*01:01:01 (count: 2746)
            2 DRB1*01:02:01 (count: 2561)
            3 DRB1*01:03 (count: 2301)
            4 DRB1*12:17 (count: 1717)
            5 DRB1*16:01:01 (count: 408)
            6 DRB1*16:02:01:02 (count: 408)
            7 DRB1*16:02:01:01 (count: 360)
            8 DRB1*15:02:01:02 (count: 300)
            9 DRB1*15:02:01:01 (count: 298)
            10 DRB1*15:01:01:02 (count: 240)

            1 ranked DRB1*01:01:01 (abundance: 100.00%)

` Thanks again and hope for your reply!