Name | Date | Size | #Lines | LOC | ||
---|---|---|---|---|---|---|
.. | 24-Jul-2020 | - | ||||
ILMN_StrandSeq/ | H | 03-May-2022 | - | 9 | 4 | |
ILMN_StrandSeq_original/ | H | 03-May-2022 | - | 9 | 4 | |
scripts/ | H | 03-May-2022 | - | 12 | 1 | |
README | H A D | 24-Jul-2020 | 1.3 KiB | 21 | 12 | |
hisatgenotype.py | H A D | 01-Jan-1970 | 0 | |||
hisatgenotype_build_genome.py | H A D | 01-Jan-1970 | 0 | |||
hisatgenotype_extract_vars.py | H A D | 01-Jan-1970 | 0 | |||
hisatgenotype_locus.py | H A D | 01-Jan-1970 | 0 | |||
hisatgenotype_locus_prev.py | H A D | 03-May-2022 | 138.6 KiB | 3,211 | 2,753 | |
hisatgenotype_modules | H A D | 01-Jan-1970 | 0 |
README
1 hisatgenotype_locus.py --aligner-list hisat2.graph --base hla --locus-list A --num-editdist 2 --assembly -1 ILMN/NA12892.extracted.1.fq.gz -2 ILMN/NA12892.extracted.2.fq.gz 2 3 for i in `ls -l CP_80/LP*1.fq.gz | awk '{print $NF}' | cut -d'/' -f2 | cut -d'.' -f1`; do echo $i; ./hisatgenotype_locus.py --locus-list A --num-editdist 2 --assembly --reads CP_80/$i.extracted.1.fq.gz,CP_80/$i.extracted.2.fq.gz --assembly-base assembly_graph_$i 2> $i.tmp; done 4 5 hisatgenotype_locus_samples.py -p 3 -v --max-sample 400 --region-list hla.A --read-dir CP_400 --out-dir test_A > cp_400_A.txt 6 hisatgenotype_scripts/compare_HLA_Omixon.py cp_400_A.txt ../CAAPA/omixon_caapa_hla.txt 7 8 hisatgenotype_locus.py --aligner-list hisat2.graph --locus-list A --num-editdist 2 --assembly -1 CP_80/LP6005106-DNA_H02.extracted.fq.1.gz -2 CP_80/LP6005106-DNA_H02.extracted.fq.2.gz --display-alleles A*23:17,A*02:02:01:01 9 10 hisatgenotype_extract_reads.py --base-fname genotype_genome --reference-type genome --read-dir ILMN_12062016 --out-dir ILMN 11 12 hisat2 --no-hd -x genotype_genome -c CAGCTGGGATGTGGAGTGGTGTGAGGAGTGGCCACAGGGGAGCAGAGGAGGTGGCAGAAGCCGGAGGTAAAGGTGTCTTAAA 13 14 15On MARCC - https://www.marcc.jhu.edu/getting-started/basic 16 17sbatch script-name 18squeue -u dkim136@jhu.edu 19scancel job-id 20sinfo 21