1 獲燃∮摹：
SRA toolkit主頁：
fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html
軟件地址：
sra-tools github: https://github.com/ncbi/sra-tools
獲取預(yù)編譯程序：
non-sudo sra-tools download:
https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit
2 下載、解壓砰诵、配置：
wget -c https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.10.9/sratoolkit.2.10.9-ubuntu64.tar.gz
tar -zxvf sratoolkit.2.10.9-ubuntu64.tar.gz
cd sratoolkit.2.10.9-ubuntu64/bin
fastq-dump --help
error
./vdb-config --interactive
tab > exit > enter 退出后：
./fastq-dump --help
/route/./fastq-dump --help
3 prefetch下載SRA數(shù)據(jù)
SRR數(shù)據(jù)
# zhengzhou
# /public/home/zzumgg03/huty/softwares/sratoolkit.2.10.9-ubuntu64/bin/./prefetch
softwares/sratoolkit.2.10.9-ubuntu64/bin/./prefetch SRR1778450
prefetch下載數(shù)據(jù)似乎有自動查重的功能雨席，已下載菩咨，或者別的程序正在下載的數(shù)據(jù)不會再次被下載，log文件似乎如此吧陡厘。
2021-02-07T08:04:56 prefetch.2.10.9: 1) Downloading 'SRR413758'...
2021-02-07T08:04:56 prefetch.2.10.9 warn: lock exists while copying file - Lock file /public/home/zzumgg03/huty/projects/diabetes/rawdata/SRR_list_
2021-02-07T08:04:56 prefetch.2.10.9: 1) failed to download 'SRR413758': RC(rcExe,rcFile,rcCopying,rcLock,rcExists)
2021-02-07T08:11:39 prefetch.2.10.9: 1) Downloading 'SRR413759'...
2021-02-07T08:11:39 prefetch.2.10.9: Downloading via HTTPS...
2021-02-08T16:09:59 prefetch.2.10.9: HTTPS download succeed
2021-02-08T16:10:10 prefetch.2.10.9: 'SRR413759' is valid
2021-02-08T16:10:10 prefetch.2.10.9: 1) 'SRR413759' was downloaded successfully
2021-02-08T16:10:10 prefetch.2.10.9: 'SRR413760' is a local non-kart file
2021-02-08T16:10:10 prefetch.2.10.9: 'SRR413761' is a local non-kart file
ERR數(shù)據(jù)
/public/home/zzumgg03/huty/softwares/sratoolkit.2.10.9-ubuntu64/bin/./prefetch ERR1190532
2022-12-21T03:16:27 prefetch.2.10.9: 1) Downloading 'ERR1190532'...
2022-12-21T03:16:27 prefetch.2.10.9: Downloading via HTTPS...
2022-12-21T03:24:36 prefetch.2.10.9: HTTPS download succeed
2022-12-21T03:25:05 prefetch.2.10.9: 'ERR1190532' is valid
2022-12-21T03:25:05 prefetch.2.10.9: 1) 'ERR1190532' was downloaded successfully
4 fastq-dump轉(zhuǎn)格式
sra2fastq
sra2fasta
sratoolkit.2.10.9-ubuntu64/bin/./fastq-dump SRR413773.sra \
--split-files \
--outdir ./
sratoolkit.2.10.9-ubuntu64/bin/./fastq-dump SRR413773.sra \
--fasta default \
--split-files \
--outdir ./
--split-files:
將雙端測序分為兩份,放在不同的文件,但是對于一方有而一方?jīng)]有的reads直接丟棄
--split-3 : 將雙端測序分為兩份,放在不同的文件,但是對于一方有而一方?jīng)]有的reads會單獨放在一個文件夾里
正常的轉(zhuǎn)格式過程是沒有中間文件產(chǎn)生的抽米，出現(xiàn)中間文件說明文件損壞，重新下載重新轉(zhuǎn)格式即可糙置。
5 fasterq-dump轉(zhuǎn)格式
sra2fastq
sratoolkit.2.10.9-ubuntu64/bin/./fastq-dump --split-3 SRR341593.sra
# real 2m17.582s
sratoolkit.2.10.9-ubuntu64/bin/./fasterq-dump \
--split-3 SRR341593.sra --threads 20 --outdir ./
# real 2m13.907s
從這里看fastq fasterq速度差不多云茸，sra為1.3Gbytes.
