How to get SRR Accession List
As you can see, sometimes we want to download a long list of datasets from a study or project, which are consisted of many runs. We need to provide the list of SRR run accessions to feed sratoolkit in order to download the sequences in them in batch mode. This makes getting a valid SRR accession list text file necessary. As we have done in this example, 'PRJNA525241_SRR_Acc_List.txt '. Where is this file from?
Luckily, now NCBI website provides a very intuitive tool to help with this task. You can follow the following steps to get the list:
- step 1: go to NCBI 'SRA Run Selector' site:
- step 2: type in the project accession or other filtering parameters, such as sample assession in 'Accession' search box, for example, we type 'PRJNA525241' and then click 'search' button:
- step 3: if the search is legitimate (means the accession number is indeed associated with some run sequence dataset(s)), then there will be a page showing all the runs in a list, with a check box on the left of each row of run detail info.
- step 4: from there you can select the interested runs by checking the checkboxs, or by click the 'check' mark at the top to select all runs, even you can filter the runs you are interested by supplying the filtering criteria on the left pane of the page.
- step 5: after you are done with selecting the runs, you can click 'Accession List' button in 'Select' section on the page, and it will initiate a download of a file called 'SRR_ACC_list', which will contain all the accession numbers you just selected. you can then use this file in sratoolkit, following the stepts the rest of this example shows.
SRA Toolkit links
Contact Information
Research Computing Services: help@scc.bu.edu
Note: RCS example programs are provided "as is" without any warranty of any kind. The user assumes the intire risk of quality, performance, and repair of any defect. You are welcome to copy and modify any of the given examples for your own use.