Results for "quality check"
Bio-Scripts
jit@jit-HP-Pro-3335-MT:~/Downloads/annotated$ sudo apt install vcftools [sudo] password for jit: Reading package...thub.io/perl_module.html # Calculate stats separately for the filter field, quali...1570 days ago
Commands to install conda in Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ mkdir jittmp jit@jit-HP-Pro-3335-MT:~/Downloads$...ountry, of encryption software. BEFORE using any encryption soft ware, please check your country's laws, regulati...1555 days ago
- jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker system df TYPE...issues Operating system: linux Perl executable at: /usr/bin/perl Please check manual. Usage: autoConT...
1553 days ago
- The procedure to find os name and version on Linux: #Open the terminal application (bash shell) #For remote server login using the ssh: ssh user@server-name #Type...
1551 days ago
Python script to check sequence length in multifasta file
#!/usr/bin/python from Bio import SeqIO import sys cmdargs = str(sys.argv) for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): output_line = '%s\t%i' % \ (seq_record.id, len(seq_record)) print(output_line)1260 days ago
Download minikraken database !
(JitMetaENV) ➜ day3 curl -O ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikraken...TE/database200mers.kmer_distrib minikraken2_v2_8GB_201904_UPDATE/hash.k2d #Check for pe reads #kraken2 --use-...1259 days ago
Create random 10000 SNPs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq SGDref.R64-2-1.dups.fa -snp...[Sun Jan 10 16:05:57 2021] Starting simuG .. [Sun Jan 10 16:05:57 2021] Check specified options .. Running...1255 days ago
Create random 1000 INDEL in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuSNP.simseq.genome.fa -i...[Sun Jan 10 16:14:00 2021] Starting simuG .. [Sun Jan 10 16:14:00 2021] Check specified options .. Running...1255 days ago
Create random 1000 CNVs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINDEL.simseq.genome.fa...[Sun Jan 10 16:24:20 2021] Starting simuG .. [Sun Jan 10 16:24:20 2021] Check specified options .. Running...1255 days ago
Create random 5 inversions in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuCNV.simseq.genome.fa -i...[Sun Jan 10 16:30:40 2021] Starting simuG .. [Sun Jan 10 16:30:40 2021] Check specified options .. Running...1255 days ago
