Results for "Tk"
Bio-Scripts
Extract ids from file with perl
#!/usr/bin/perl use strict; use warnings; my $fh=read_fh("fin.txt"); my %idHash; my $lastKey; while () { chomp $_; my @cells = split /\t/, $_; $idHash{$cells[0]}=$....2602 days ago
Plot custom gene density with R
library(karyoploteR) pp2244 days ago
Perl script to find palindromic regions in DNA sequences
use strict; use warnings; my $pp = qr/(?: (\w) (?1) \g{-1} | \w? )/ix; my $filename = $ARGV[0]; open(my $fh, '2148 days ago
- ...nput files. (both directions in parallel)CMD: seqtk-trinity seq -A /media/urbe/My...CXX.IND11_noribo_clean.fastq >> left.fa CMD: seqtk-trinity seq -A /media/urbe/My...ir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A - >> left.fa...
2121 days ago
Installing Busco version 4.0.6
...da suitesparse-5.2.0 | h9e4a6bb_0 2.4 MB tktable-2.10 |...suitesparse pkgs/main/linux-64::suitesparse-5.2.0-h9e4a6bb_0 tktable pkgs/main/lin...1447 days ago
- ...//github.com/broadinstitute/gatk/releases/download/4.0.2.1/gatk-4.0.2.1.zip --2018-08-30 11:...dra@jitendra-UNLOCK-INSTALL[gatk-4.0.2.1] ./gatk --list...Compare GATK's internal pileup to a refere...reads. MarkDuplicatesGATK (EX...
2069 days ago
Installing pb-assembly on Linux !
...OpenFOAM/2.0.x/DP FLTK/1.3.3-foss-2016a...Tk/8.6.4-foss-2016a-no-X11 Java...3.25.2 hb1c47c0_0 conda-forge tk 8.6.8...2028 days ago
Setting up falconUnzip conda environments for genome assembly !
...forge six: 1.11.0-py27_1001 conda-forge sqlite: 3.25.3-hb1c47c0_0 conda-forge tk: 8.6.9-h...1984 days ago
Palindrome Simulation commands !
...Tools/art_bin_MountRainier/art_illumina -ss MSv3 -sam -i allPalindromeSimulated.fa -p -l 250 -f 100 -m 300 -s 10 -o paired_dat 3321 ~/Tools/seqtk/seqtk mergepe paired_dat1.fq paired...1730 days ago
- # Convert FASTQ to FASTA seqtk seq -a IN.fastq > OUT.fasta # Convert FASTQ to FASTA and set bases of quality lower than 20 to N seqtk seq -aQ64 -q20 -n N IN.fastq > OUT.fasta # Download Seqtk https://github.com/lh3/seqtk
1719 days ago
