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DaehwanKimLab / hisat-genotype

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update DB #60

Open ghost opened 2 years ago

ghost commented 2 years ago

Hello, I am trying to update the hla db but without succeeding, could you help me with the commands? I downloaded the files fasta, msf and hla.dat, replaced those present in the hisatgenotype_db / HLA directory. Once the analysis is finished, the result is always the same as before the update

thank you

chbe-helix commented 2 years ago

Hi vcaldara,

I suspect HISATgenotype is still pointing to to old database. Can you describe how it is installed and how you are using the new Database?

Thanks, Chris

ghost commented 2 years ago

Hi Mr. Bennett I installed hisatgenotype on a centos 8 system via github as described here https://daehwankimlab.github.io/hisat-genotype/tutorials/#initial-setup. Then I updated the DB by downloading the fasta and msf and hla.dat files from https://github.com/ANHIG/IMGTHLA. I use the DB with basic command "hisatgenotype --base hla --locus-list A,....... -1 ...... -2 ......." Maybe my problem is how to create the Building a Graph Reference and Index and its base ? Can you help me ?

shiwanyin commented 2 years ago

Hi Mr. Bennett I installed hisatgenotype on a centos 8 system via github as described here https://daehwankimlab.github.io/hisat-genotype/tutorials/#initial-setup. Then I updated the DB by downloading the fasta and msf and hla.dat files from https://github.com/ANHIG/IMGTHLA. I use the DB with basic command "hisatgenotype --base hla --locus-list A,....... -1 ...... -2 ......." Maybe my problem is how to create the Building a Graph Reference and Index and its base ? Can you help me ?

HI vcaldara I also have the same problem.
Did you solve it now ?

shiwanyin commented 2 years ago

Hi vcaldara,

I suspect HISATgenotype is still pointing to to old database. Can you describe how it is installed and how you are using the new Database?

Thanks, Chris

Hi, Mr. Bennet i have the same problem,too. and when i look for the closed issues, Updating hisatgenotype_db #12 successfully update the db. But i do not know how to update it. I have tried vcaldara's way but it failed.

ghost commented 2 years ago

Hi Mr. Bennett I installed hisatgenotype on a centos 8 system via github as described here https://daehwankimlab.github.io/hisat-genotype/tutorials/#initial-setup. Then I updated the DB by downloading the fasta and msf and hla.dat files from https://github.com/ANHIG/IMGTHLA. I use the DB with basic command "hisatgenotype --base hla --locus-list A,....... -1 ...... -2 ......." Maybe my problem is how to create the Building a Graph Reference and Index and its base ? Can you help me ?

HI vcaldara I also have the same problem. Did you solve it now ?

Hi, shiwanyin no, unfortunately i was not able to solve, I am still waiting for a kind reply I also tried to rebuilding a Graph Reference and Index without success, but one question at a time

shiwanyin commented 2 years ago

Hi Mr. Bennett I installed hisatgenotype on a centos 8 system via github as described here https://daehwankimlab.github.io/hisat-genotype/tutorials/#initial-setup. Then I updated the DB by downloading the fasta and msf and hla.dat files from https://github.com/ANHIG/IMGTHLA. I use the DB with basic command "hisatgenotype --base hla --locus-list A,....... -1 ...... -2 ......." Maybe my problem is how to create the Building a Graph Reference and Index and its base ? Can you help me ?

HI vcaldara I also have the same problem. Did you solve it now ?

Hi, shiwanyin no, unfortunately i was not able to solve, I am still waiting for a kind reply I also tried to rebuilding a Graph Reference and Index without success, but one question at a time

Thanks !