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jonassibbesen / vgrna-project-paper

Bash scripts and data used in pantranscriptomic paper
MIT License
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Make pantranscriptome for HLA region - IGMT? #3

Open Giang961 opened 1 year ago

Giang961 commented 1 year ago

Hi Jonassibbesen ! In add_haplotype.sh of making pantranscriptome for 1kg_all_af001_imgt_hla_p10k_noB258_noN_a100_gencode100 : -using this command line : "aws s3 cp s3://vg-k8s/users/jsibbesen/vgrna/benchmark/whole_genome/data/graphs/${GRAPHS_PREFIX}/6/${GRAPHS_PREFIX}_6.pg 6.pg --no-progress"

This GRAPH_PREFIX should be "1kg_all_af001_gencode100"?

Thanks

jonassibbesen commented 1 year ago

Hi,

Yes, the HLA graph and pantranscriptome (1kg_all_af001_imgt_hla_p10k_noB258_noN_a100_gencode100) was created from the graph 1kg_all_af001_gencode100.

The 1kg_all_af001_imgt_hla_p10k_noB258_noN_a100_gencode100 graph and pantranscriptome is available to download here: http://cgl.gi.ucsc.edu/data/vgrna/pantranscriptomes/1kg_all_af001_imgt_hla_p10k_noB258_noN_a100_gencode100/

Please let me know if you have any other questions.