1831 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting sam file into fasta samtools fasta reads_mapped.sam > reads.fasta ### convertin...1600 days ago
1550 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.gz SRR1770413_2.fastq.gz \ | samtools view -b - >SRR1770413.raw.bam sambamb...1556 days ago
Install Nucmer on Linux / Ubuntu
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt install mummer [sudo] password for jit: Reading package lists... Done Building dependency tree...1547 days ago
Install python pip and numpy on Linux / Ubuntu
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt install python-pip Reading package lists... Done Building dependency tree...1547 days ago
Install miniasm in Linux / Ubuntu
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter$ sudo apt install miniasm Reading package lists... Done Building dependency tree...1547 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencing data. PROJECT=PRJNA257197 # The number of datasets to subselect from the projec...1539 days ago
1538 days ago
Install python-numpy python-scipy python-matplotlib on Ubuntu !
$MT:~/Downloads/chaos$ sudo apt-get install python-numpy python-scipy python-matplotlib Reading package lists... Done Building dependency tree...1538 days ago