ljxue的个人博客分享 http://www.blog.sciencetimes.com.cn/u/ljxue Liangjiao Xue, Bioinformatics is my favorite.

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向NCBI SRA提交数据

已有 9444 次阅读 2014-11-15 05:17 |个人分类:Bioinformatics|系统分类:科研笔记| NCBI, SRA

0 Collect description information, prepare read files.

   Run md5sum (Linux) to get the md5 numbers of read files

1 Create BioProject

      Go to: http://www.ncbi.nlm.nih.gov/books/NBK47529/

      "Steps for SRA Submission"-->Create a BioProject for this research

      click the link of BioProject .

      On the new page, clike "New submission".

2 Create BioSample


      Go to: http://www.ncbi.nlm.nih.gov/books/NBK47529/

      "Steps for SRA Submission"-->Create a BioSample submission for your biological sample(s)

      click the link of BioSample  .

      On the new page,  click "Download batch template" next to "New submission".

       Edit the file to inlcude the information of your samples.

       clike "New submission".

       Check the submitter information, and select "multiple samples"

       Load the batch file describing your samples.

       Make necessary modification according to information of  error detection.

       

   You need to wait for hours to get offical accessions.
   (PRJNAxxxxxx for BioProject and SAMNxxxx for BioSample)


3 New Experiment

   Go to:

   http://www.ncbi.nlm.nih.gov/Traces/sra_sub/sub.cgi

  Click the project you want to add Experiment

  Click "New Experiment" in the new page.

  (You could get the same page by clickin these links).

  (SRA -> Submit->Submission->New Experiment)

4 New run

   Click "New run" in the SRA project page.

   Get the password

Put files onto SRA sever.


     cd   datadirectoryonlocalsever

         ftp -i  ftp-private.ncbi.nih.gov  

         Login: sra

         Password: 03o4!srRy! (you need new one)

         (ftp -i : -i was used suppress confirmation)

         mkdir PRJNA247388

         cd    PRJNA247388

         mput *.gz  

         mput *.fastq


5 Link the files in Runs.

If you have more than 25 BioSamples, send an email to SRA.

You also need to transfer the data using the command listed earlier.


http://www.ncbi.nlm.nih.gov/books/NBK47529/

 




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