Results for "BED files"
Bio-Scripts
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_1.fas...reference file name (bwa finds the indexes using this) and the input alignment files. The first file should contai...1554 days ago
Install Nucmer on Linux / Ubuntu
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt install mummer [sudo] pass...s) Selecting previously unselected package gawk. (Reading database ... 186076 files and directories currently ins...1545 days ago
Install python pip and numpy on Linux / Ubuntu
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt...libexpat1-dev:amd64. (Reading database ... 186309 files and directories currently ins...tall numpy Collecting numpy Downloading https://files.pythonhosted.org/packages/3a/...1545 days ago
Install miniasm in Linux / Ubuntu
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt install miniasm Reading pa...Selecting previously unselected package miniasm. (Reading database ... 187073 files and directories currently ins...1545 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/b...ross compiling... no checking for suffix of object files... o checking whether we are...r egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/type...1545 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR Bi...parallel fastq-dump -O reads -X 1000 --split-files {} # Create a directory for bam files mkdir -p bam # Generate a...tract reads, tagged with readgroups to paired files. samtools fastq -t -1 all1.f...1537 days ago
- $MT:~/Downloads/cgr-perl$ sudo apt-get install gnuplot [sudo] password for jit:...y unselected package libdouble-conversion1:amd64. (Reading database ... 189871 files and directories currently ins...
1536 days ago
Install python-numpy python-scipy python-matplotlib on Ubuntu !
$MT:~/Downloads/chaos$ sudo apt-get install python-numpy python-scipy python-matplo...cting previously unselected package tk8.6-blt2.5. (Reading database ... 190390 files and directories currently ins...1536 days ago
- jit@jit-HP-Pro-3335-MT:~$ java -version openjdk versio...package python3-smbc. (Reading database ... 192946 files and directories currently ins...package samba-common. (Reading database ... 192954 files and directories currently ins...
1534 days ago
- jit@jit-HP-Pro-3335-MT:~/Downloads/annotated$ sudo apt install vcftools [sudo] pas...Selecting previously unselected package vcftools. (Reading database ... 193392 files and directories currently ins...
1520 days ago
