Question

how to get SRA data

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7.4 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 • 4.4k views

ADD COMMENT • link updated 7.4 years ago by bongok ▴ 40 • written 7.4 years ago by mra8187 ▴ 20

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

ADD REPLY • link 7.4 years ago by GenoMax 141k

score 1 · Answer 1 · 2016-12-14

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7.4 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 • link 7.4 years ago by Chun-Jie Liu ▴ 280

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

ADD REPLY • link 7.4 years ago by GenoMax 141k

score 0 · Answer 2 · 2016-12-14

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7.4 years ago

Benn 8.3k

You can use sra toolkit for it:

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

ADD COMMENT • link 7.4 years ago by Benn 8.3k

score 0 · Answer 3 · 2016-12-14

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7.4 years ago

bongok ▴ 40

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

ADD COMMENT • link 7.4 years ago by bongok ▴ 40