Man pages for yangjl/huskeR
Genomic and Genetic analysis Pipeline on HPC
| convert_gbs2plink | 'Change gbs hmp to plink format' |
| plot_mht | 'manhattan plot' |
| plot_stack | 'Stacking plot with 10 maize chromosomes' |
| run_aspera | 'Run Aspera Connect to download from SRA.' |
| run_bismark | 'Run array Bismark job on farm' |
| run_bwamem | 'Run BWA-mem job on farm' |
| run_fastq_qc | 'Run fastq QC.' |
| run_fq_dump | 'Run fastq-dump.' |
| run_GATK | 'Run GATK array jobs on HPC' |
| run_GBSv2 | 'Run TASSEL GBSv2 on slurm-based HPC' |
| run_gctb | 'Run GCTB in a wrapper developed by Jinliang Yang Lab at... |
| run_gemma | 'Run serial gemma jobs on slurm-based HPC' |
| run_GenSel4 | 'Run GenSel on slurm-based HPC' |
| run_kallisto | 'Run kallisto quant.' |
| run_ldak | 'Set up aspera code in a job shell' |
| run_Rcode | 'Run array job of R codes' |
| run_VCAP | 'Run VCAP array jobs on HPC' |
| set_array_job | 'Set up array job on farm' |
| set_slurm_job | 'Set up one farm job' |
