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precimed / pleiofdr

Pleiotropy-informed conditional and conjunctional false discovery rate
GNU General Public License v3.0
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Question about generating reference based on East Asian individuals of 1000 genome #17

Open LDHHAHA opened 1 year ago

LDHHAHA commented 1 year ago

Hi there,

I try to generate reference data based on East Asian individuals of 1000 Genomes. I followed your steps (https://precimed.s3-eu-west-1.amazonaws.com/pleiofdr/about.txt). I completed every step before "# ref9545380_1kgPhase3eur_LDr2p1.mat was created using the following scripts:" (Line 73 in about.txt). However, one of the input files in the later script could not be found （"template.1000genomes503eur9m.sorted.complete_annot_hg19.annomat.uniq.ld_informed.txt.gz"，line 99 in about.txt）. Could you please show me how to prepare this file? Any help is appreciated. Thank you!

dqwssy commented 1 year ago

Hi there,

I try to generate reference data based on East Asian individuals of 1000 Genomes. I followed your steps (https://precimed.s3-eu-west-1.amazonaws.com/pleiofdr/about.txt). I completed every step before "# ref9545380_1kgPhase3eur_LDr2p1.mat was created using the following scripts:" (Line 73 in about.txt). However, one of the input files in the later script could not be found （"template.1000genomes503eur9m.sorted.complete_annot_hg19.annomat.uniq.ld_informed.txt.gz"，line 99 in about.txt）. Could you please show me how to prepare this file? Any help is appreciated. Thank you!

Hello, is this problem solved? I'm having the same difficulty, maybe we can share some information. Thanks for any help.

LDHHAHA commented 1 year ago

Hi there, I try to generate reference data based on East Asian individuals of 1000 Genomes. I followed your steps (https://precimed.s3-eu-west-1.amazonaws.com/pleiofdr/about.txt). I completed every step before "# ref9545380_1kgPhase3eur_LDr2p1.mat was created using the following scripts:" (Line 73 in about.txt). However, one of the input files in the later script could not be found （"template.1000genomes503eur9m.sorted.complete_annot_hg19.annomat.uniq.ld_informed.txt.gz"，line 99 in about.txt）. Could you please show me how to prepare this file? Any help is appreciated. Thank you!

Hello, is this problem solved? I'm having the same difficulty, maybe we can share some information. Thanks for any help.

Not yet. Sure, here is my email, lidh@sysucc.org.cn

xiangboyulan commented 4 months ago

Hi there, I try to generate reference data based on East Asian individuals of 1000 Genomes. I followed your steps (https://precimed.s3-eu-west-1.amazonaws.com/pleiofdr/about.txt). I completed every step before "# ref9545380_1kgPhase3eur_LDr2p1.mat was created using the following scripts:" (Line 73 in about.txt). However, one of the input files in the later script could not be found （"template.1000genomes503eur9m.sorted.complete_annot_hg19.annomat.uniq.ld_informed.txt.gz"，line 99 in about.txt）. Could you please show me how to prepare this file? Any help is appreciated. Thank you!

Hello, is this problem solved? I'm having the same difficulty, could you share some information for me. Thanks a lot.

my email, xiangbo@swmu.edu.cn