how to get SRA data
3
0
Entering edit mode
7.9 years ago
mra8187 ▴ 20

Dear all

how can i get this data from ncbi ? https://www.ncbi.nlm.nih.gov/sra/SRX1835119[accn] thank you

genome • 4.6k views
ADD COMMENT
0
Entering edit mode

Use SRAToolkit based on instructions here. Otherwise you can search EBI-ENA and download fastq's from there directly.

ADD REPLY
1
Entering edit mode
7.9 years ago
Chun-Jie Liu ▴ 280

A simple script to use lftp to download SRA data. Then use fastq-dump to decompress data

SRAToolkit download and decompress data at same time. If you have many sra data to download. You can use the script to download and decompress youself in parallel.

ADD COMMENT
0
Entering edit mode

As long as this is kept is mind: A: fastq dump error

ADD REPLY
0
Entering edit mode
7.9 years ago
Benn 8.3k

You can use sra toolkit for it:

https://www.ncbi.nlm.nih.gov/books/NBK158899/

ADD COMMENT
0
Entering edit mode
7.9 years ago
bongok ▴ 40

Or use SRAdb in R bioconductor. How To Download All Sra Samples At Once ?

ADD COMMENT

Login before adding your answer.

Traffic: 2350 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6