Results for "DU"
Bio-Scripts
Bash script to handle Multifasta files
#Convert all lowercase residues to uppercase in a FASTA sequence file $ awk 'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $1}}' input.fasta > output.fasta #Rearrange...1359 days ago
- (JitMetaENV) ➜ JitMeta conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.
1219 days ago
- (JitMetaENV) ➜ ~ conda install -c bioconda quast Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer vers...
1217 days ago
- (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen...
1217 days ago
Download minikraken database !
(JitMetaENV) ➜ day3 curl -O ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikraken2_v2_8GB_201904.tgz % Total % Received % Xferd Average Speed Time Time Time Cu...1216 days ago
Create random 10000 SNPs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq SGDref.R64-2-1.dups.fa -snp_count 10000 -prefix...0.5 [Sun Jan 10 16:05:57 2021] Introducing random SNPs based on the...pondance map for genomic variants introduced during simulation: simuSN...1213 days ago
Create random 1000 INDEL in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuS..._constant = 0.5 [Sun Jan 10 16:14:00 2021] Introducing random INDELs based on th...ng the correspondance map for genomic variants introduced during simulation: simuIN...1213 days ago
Create random 1000 CNVs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -ref...een specified: cnv_count = 100 The option duplication_tandem_dispersed_ratio has been specified: duplication_tandem_dispersed_rat...rrespondance map for genomic variants introduced during simulation: simuCN...1213 days ago
Create random 5 inversions in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuC...x_size = 100000 [Sun Jan 10 16:30:40 2021] Introducing random Inversions based o...ng the correspondance map for genomic variants introduced during simulation: simuIN...1213 days ago
Create random 2 translocations in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuI...ation_count = 2 [Sun Jan 10 17:12:58 2021] Introducing random Translocations bas...ng the correspondance map for genomic variants introduced during simulation: simuTR...1213 days ago
