Results for "binary files"
Bio-Scripts
Samtools commands for bioinformatician !
...-o sal_sej.bam sal_sej.sam ### viewing bam files (view command) samtool view s...le # ouput is file.bai # always index sorted files samtools index sal_sej_sorte...iants (mpileup command) # -g : output is bcf (binary call format) file # -f : us...1617 days ago
- $ sudo apt install npm Reading package lists... Done Building dependency tree...0% Selecting previously unselected package gyp. (Reading database ... 180389 files and directories currently ins...
1567 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pull...quencing run ID fastq-dump --split-files SRR1770413 #SRA stores dat...Q for further processing. The --split-files part of the command ensures w...0413/SRR1770413.sra sra-dump --split-files SRR1770413.sra1573 days ago
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.fastq...reference file name (bwa finds the indexes using this) and the input alignment files. The first file should contai...1573 days ago
Install Nucmer on Linux / Ubuntu
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt install mummer [sudo] passwo...) Selecting previously unselected package gawk. (Reading database ... 186076 files and directories currently ins...1564 days ago
Install python pip and numpy on Linux / Ubuntu
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt in...libexpat1-dev:amd64. (Reading database ... 186309 files and directories currently ins...tall numpy Collecting numpy Downloading https://files.pythonhosted.org/packages/3a/...1564 days ago
Install miniasm in Linux / Ubuntu
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt install miniasm Reading pack...Selecting previously unselected package miniasm. (Reading database ... 187073 files and directories currently ins...1564 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/bin$...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...1564 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioP...parallel fastq-dump -O reads -X 1000 --split-files {} # Create a directory for bam files mkdir -p bam # Generate a...ract reads, tagged with readgroups to paired files. samtools fastq -t -1 all1.f...1556 days ago
- $MT:~/Downloads/cgr-perl$ sudo apt-get install gnuplot [sudo] password for jit: Re...unselected package libdouble-conversion1:amd64. (Reading database ... 189871 files and directories currently ins...
1555 days ago
