Sequence Read Archive (SRA)

2021.8.13 HuPY

1. OverView

Prepare the following information for your submission and be ready to:

1. Provide a project name and description

2. Choose the type or ‘package’ of your samples

3. Provide sample metadata that is unique by sample

4. Provide sequence metadata

5. Upload your files

2. Project

For a new project, prepare the information that creates a BioProject.

Required information:

1. Title

2. Description

Optional information:

1. Participants

2. Grants: Required if your project was funded by a National Institutes of Health (NIH) grant

Important: The required BioProject and BioSample can be created during submission. You can also link an existing BioProject and BioSample with accession numbers.

3. Sample

For new samples, prepare the details that will serve as BioSamples' metadata for individual biological specimens (collection date, location, etc.).

1. Select the ‘package’ that best fits your biological samples. Each package has a distinct set of required attributes which you can preview here.

   Take ’Metagenome‘ for example：

2. Each sample must have a unique set of attributes. Provide all required fields and any optional fields that apply to your samples.

3. Add custom attributes to fully describe your samples and facilitate searching. You should submit at least one unique data file for each sample you create.

4. Library

Prepare the following 'Library' information:

1. Which BioSample should be linked to which file(s)

2. Your library construction protocol

3. Other metadata like unique library names, sequencing platform, and filetype

• Reference： About Sequence Read Archive (SRA) Submission (nih.gov)

5.Summary

1. BioSample is an description file.

   BioProject related to SRA & BioSample

   --- N BioSample

   --- Biosamples： SRSxxx

   --- N SRA

   --- Experiments: SRXxxx

   --- Runs: SRRxxx

2. Batch-download from SRA

   1. 在文章Data Availability部分查找文章对应的BioProject ID，然后进入SRA Run Selector网址，在”Accession“搜索栏中输入BioProject ID即可获得研究所有相关的SRR...。

   2. 在Found xx items一栏中勾选所有Run，然后点击上方的Select栏目的Selected中的 Metadata （named SraRunTable）或Accession list（named SRR_Acc_List）获取相对应的文件。使用FileZilla软件传输上述两个文件（path：~/paper_code/pnasHeterosis）。

   3. 接着在集群中批量下载数据

   <pre class="md-fences md-end-block ty-contain-cm modeLoaded" spellcheck="false" lang="bash" cid="n306" mdtype="fences" style="box-sizing: border-box; overflow: visible; font-family: var(--monospace); font-size: 0.9em; display: block; break-inside: avoid; text-align: left; white-space: normal; background-image: inherit; background-position: inherit; background-size: inherit; background-repeat: inherit; background-attachment: inherit; background-origin: inherit; background-clip: inherit; background-color: rgb(248, 248, 248); position: relative !important; border: 1px solid rgb(231, 234, 237); border-radius: 3px; padding: 8px 4px 6px; margin-bottom: 15px; margin-top: 15px; width: inherit; color: rgb(51, 51, 51); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-style: initial; text-decoration-color: initial;"># 加载环境变量
   modules

   加载sratoolkit

   module load sratoolkit/2.9.6

   检查sratoolkit 可否正常使用

   prefetch --help

   进入工作路径“~/paper_script/pnasHeterosis”,使用sratoolkit批量下载

   cd ~/paper_script/pnasHeterosis

   Alias:alias BSUB="echo 'bsub -J blast -n 2 -R span[hosts=1] -o %J.out -e %J.err -q normal 'command''"

   BSUB

   下载的数据默认路径为"~/ncbi/public/sra"

   </pre>

   Command line

   <pre mdtype="fences" cid="n319" lang="bash" spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" style="box-sizing: border-box; overflow: visible; font-family: var(--monospace); font-size: 0.9em; display: block; break-inside: avoid; text-align: left; white-space: normal; background-image: inherit; background-position: inherit; background-size: inherit; background-repeat: inherit; background-attachment: inherit; background-origin: inherit; background-clip: inherit; background-color: rgb(248, 248, 248); position: relative !important; border: 1px solid rgb(231, 234, 237); border-radius: 3px; padding: 8px 4px 6px; margin-bottom: 15px; margin-top: 15px; width: inherit; color: rgb(51, 51, 51); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-style: initial; text-decoration-color: initial;">#!/bin/sh
   bsub -J prefetch -n 2 -R span[hosts=1] -o %J.prefetch.out -e %J.prefetch.err -q normal 'prefetch --option-file ~/paper_script/pnasHeterosis/SRR_Acc_List.txt'
   bsub -K -J fastqdump -n 2 -R span[hosts=1] -o %J.fastqdump.out -e %J.fastqdump.err -q normal 'fastq-dump -I --split-files ~/ncbi/public/sra/*sra'</pre>