Glucoma-variant-calling/Fayrouz at master · marwaabdelazim/Glucoma-variant-calling · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13

***Install SRAtoolkit***
https://ncbi.github.io/sra-tools/fastq-dump.html
file:///home/fayrouz/Downloads/SRA-Tools%20-%20Installation%20and%20Configuration.html

wget "http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-centos_linux64.tar.gz"
tar -xzf sratoolkit.current-centos_linux64.tar.gz
cd sratoolkit/ cd bin
./fastq-dump
sudo apt sratoolkit (it was asked to install)
./vdb-config -i # (enable remote access- enter- save- exit)
***down load 15 million reads for PCAG sample  (SRR5858157) R1&R2) by using the fastq dump
fastq-dump -X 15000000 -Z SRR5858157 |fastq-dump -I --split-files SRR5858157