Results for "r"
Bio-Scripts
Install asciigenome using conda !
(JitMetaENV) ➜ viruses conda install -c bioconda asciigenome Collecting package metadata (current_repodata.json): / done Solving environment: done ==> WARNING: A newer version of conda exists.1276 days ago
Download minikraken database !
(JitMetaENV) ➜ day3 curl -O ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikraken2_v2_8...(JitMetaENV) ➜ day3 ls minikraken2_v2_8GB_201904.tgz (JitM.... (JitMetaENV) ➜ krakenDB tar -xvzf minikraken2_v2_8GB_2019....fastq.gz ../mappings/evol1.sorted.unmapped.R2.fastq.gz > evo...1275 days ago
- (JitMetaENV) ➜ day3 conda install -c bioconda krona Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. 2020.12.5-py36h5fab9bb_1 Proceed ([y]/n)?
1275 days ago
- ...bioconda maxbin2 Collecting package metadata (current_repodata.json): done Solv...olve. Retrying with flexible solve. Solving environment: failed with repodata f...son): done Solving environment: done ==> WARNING: A newer version of conda...
1275 days ago
Create random 10000 SNPs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq SGDref.R...Check specified options .. Running simuG for SNP/INDEL sim...ount = 10000 The option titv_ratio has been specified: titv_....refseq2simseq.map.txt Generating reference-based vcf file...1272 days ago
Create random 1000 INDEL in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuSNP....Check specified options .. Running simuG for SNP/INDEL sim...nt = 1000 The option ins_del_ratio has been specified: ins_d...w_alpha = 2 > indel_size_powerlaw_constant = 0.5 [Sun Jan...1272 days ago
Create random 1000 CNVs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINDE...Check specified options .. Running simuG for CNV simulatio...ption duplication_tandem_dispersed_ratio has been specified:..._count = 100 > cnv_gain_loss_ratio = 1 > duplication_tandem...1272 days ago
Create random 5 inversions in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuCNV.simseq.genome.fa -inversion_count 5 -prefix simuINV...Check specified options .. Running simuG for inversion sim...un Jan 10 16:30:40 2021] Generating output files .. Gener...1272 days ago
Create random 2 translocations in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINV.simseq.genome.fa -translocation_count 2 -prefix si...Sun Jan 10 17:12:58 2021] Starting simuG .. [Sun Jan 10 1...ed: 1925195826 The option translocation_count has been spe...files .. Generating the correspondance map for genomic va...1272 days ago
- (JitMetaENV) ➜ wgd git:(master) pip install --user ERROR: You must give at least one requirement to install (see "pi...lib/python3.6/site-packages (from matplotlib>=3.0.2->wgd==1.2...uninstalled pandas-1.0.5 WARNING: The script humanfriendly...
1269 days ago
