linux 下载sra数据库,从ncbi下载sra数据的几种种方式

为了加快速度先下载aspera并添加环境变量，具体看以前的内容

下载sra toolkit加环境变量

下载EDirect

用yeast的几个数据说明

1. 直接用run id

prefetch SRR1553610

2. 写入文件下载

echo SRR1553608 > sra.ids

echo SRR1553605 >> sra.ids

prefetch --option-file sra.ids

3 利用sed和bash

cat sra.ids|sed 's/SRR/fastq-dump --split-files SRR/'|bash

4 通过EDirect获取runinfo

esearch -db sra -query PRJNA257197 | efetch -format runinfo > runinfo.txt

$ cat runinfo.txt |head

Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash

SRR1972917,2015-04-14 13:59:24,2015-04-14 13:56:53,4377867,884329134,4377867,202,486,,https://sra-download.ncbi.nlm.nih.gov/traces/sra27/SRR/001926/SRR1972917,SRX994194,G5723.1.l1,RNA-Seq,cDNA,TRANSCRIPTOMIC,PAIRED,0,0,ILLUMINA,Illumina HiSeq 2500,SRP045416,PRJNA257197,2,257197,SRS908519,SAMN03254208,simple,186538,Zaire ebolavirus,G5723.1,,,,,,,no,,,,,BI,SRA178666,,public,4C15DC4E43EA2DD6DA211DCDB3E400F0,94BEB800D624CB20C04DD09D0C56BC86

SRR1972918,2015-04-14 13:58:26,2015-04-14 13:56:34,3856384,778989568,3856384,202,457,,https://sra-download.ncbi.nlm.nih.gov/traces/sra27/SRR/001926/SRR1972918,SRX994195,G5731.1.l1,RNA-Seq,cDNA,TRANSCRIPTOMIC,PAIRED,0,0,ILLUMINA,Illumina HiSeq 2500,SRP045416,PRJNA257197,2,257197,SRS908518,SAMN03254209,simple,186538,Zaire ebolavirus,G5731.1,,,,,,,no,,,,,BI,SRA178666,,public,63AE692146061962D2BA889EAF5A86CA,F910CC0D2C1F588AD0EB8C1DDE93AD14

......

所以需要提取,分隔的第一列，并且grepSRR开头的数据

cat runinfo.txt | cut -f 1 -d ","|grep SRR > sra.ids

然后下载即可,注意不要下载，这只是示例，因为里面包含大量数据，如果想下载看下空间du -hs ~/ncbi

prefetch --option-file sra.ids

5 继续bash

cat sra.ids|sed 's/SRR/fastq-dump --split-files SRR/' |bash

这样就得到了PRJNA25719的所有测序数据