old fastq-dump

NCBI SRA download


update 2018: consider using the new version → fasterq-dump


fastq-dump can be used for local .sra files or for direct download from NCBI

# local use (path to .sra file)

fastq-dump --split-spot path/to/local/file/SRR649944.sra

SRR649944.fastq

# direct download from NCBI/SRA (only accession number, no path)

fastq-dump --split-3 SRR649944

SRR649944_1.fastq

SRR649944_2.fastq

A .sra file copy will be saved to a local cache/archive folder, used for repeated fastq-dump calls without re-download

$HOME/ncbi/public/sra/SRR649944.sra

Download only

A) fasterq-dump

B) prefetch

Alternatively, prefetch can be used for only downloading the .sra file for later use by fastq-dump

prefetch SRR649944 # stores .sra file in $HOME/ncbi/public/sra/

fastq-dump --split-3 SRR649944 # takes file from $HOME/ncbi/public/sra/ (without download again)

SRR649944_1.fastq

SRR649944_2.fastq

C) wget (not recommended)

Download error

In case of download error, a cache and/or lock file may need to be removed, before trying again

rm $HOME/ncbi/public/sra/SRR649944.sra.cache

rm $HOME/ncbi/public/sra/SRR649944.sra.cache.lock

rm $HOME/ncbi/public/sra/SRR649944.sra.tmp.23569.tmp # prefetch

http://www.ncbi.nlm.nih.gov/books/NBK158899/#SRA_download.downloading_sra_data_using


fastq-dump options


Extracting fastq files from SRA files, for paired-end reads

fastq-dump --split-3 SAMPLE

results:

SAMPLE_1.fastq

SAMPLE_2.fastq

SAMPLE.fastq (only if .sra contains single reads / single-end sequencing)

--split-3 splits paired reads into files *_1.fastq and *_2.fastq; single read (if any) into *.fastq

SAMPLE can be a SRA-id (download from NCBI or local ncbi/public/sra/ archive) or direct path to local .sra file

fastq-dump --split-3 SRR649944

fastq-dump --split-3 path/to/local/file/SRR649944.sra


Converting SRA files into a single fastq file

fastq-dump --split-spot SAMPLE

results:

SAMPLE.fastq

options:

--split-spot split paired-end reads, but writes all to a single fastq file


To use in a pipe

fastq-dump -Z --split-spot SAMPLE | bowtie2 ...

options:

-Z writes sequences to standard output


Filter read length of SRA samples

fastq-dump --minReadLen 80 --split-3 SAMPLE

fastq-dump --minReadLen 80 --split-spot -Z SAMPLE | bowtie2 ...

options:

--minReadLen 80 extracts only reads >= 80bp from SRA file


read more

http://ncbi.github.io/sra-tools/fastq-dump.html

https://github.com/ncbi/sra-tools/wiki/HowTo:-Access-SRA-Data

http://www.ncbi.nlm.nih.gov/books/NBK47528/

http://www.ncbi.nlm.nih.gov/books/NBK242621/#_SRA_Download_Guid_BK_The_SRA_Toolkit_

http://www.ncbi.nlm.nih.gov/books/NBK158899/#SRA_download.downloading_sra_data_using