Results for "Bioinformatics Scripts"
Bio-Scripts
# Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe192257 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM fil...ipt (https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obta.... https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py2117 days ago
- #!/bin/bash #set the path export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/bin export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/scripts export AUGUSTUS_CONFIG_PAT...
2130 days ago
Installing Platypus on Ubuntu !
(py27) ➜ Tools git:(master) ✗ git clone https://github.com/andyrimmer/Platypus.git...le extensions LICENSE Makefile misc README.md release sanityChecks.py scripts src test ➜ Platypus git...2012 days ago
Installing docker for Bioinformatics on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove docker docker-engine docker.io containerd runc Reading package lists... Done Building dependency tree...1506 days ago
Pack a perl program with their dependencies on Ubuntu !
...can find the test script web.pl at https://bioinformaticsonline.com/snippets/view/41440...~/Downloads/autoConTAMPR/bin$ ./web https://bioinformaticsonline.com #It return thi...yResearchLabsQuestionsPagesDiscussionMoreBioScriptsBlogsBookmarksFilesFunGroupsPo...1504 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
#Need to download i-adhore-3.0.01.tar.gz from https://wdiceryfd4rjn74bjhhtz2k5di--bioinformatics-psb-ugent-be.translate.goog/webtools/i-adhore/licensing/ #Follow these steps (wgd) ➜ i-adh...1197 days ago
Bash script to check installed bioinformatics program !
allTools=(bwa mummer trimomatic) decFlag=0; for name in ${allTools[@]}; do #echo "enter your package name" # read name dpkg -s $name &> /dev/null...1039 days ago
- #R is a feature rich interpretive programming language originally released in 1995. It is heavily used in the bioinfo...
816 days ago
