Changes between Version 3 and Version 4 of SOPs/qc_SRA

Timestamp:

08/25/20 11:43:52 (4 years ago)

Author:

gbell

Comment:

--

SOPs/qc_SRA

@@ -54 +54 @@
 === Downloading and processing multiple NCBI SRA samples ===
 
-To '''download a list of SRR files''' (such as for all of the samples of a data series) from NCBI, use prefetch.
+To download a list of SRR files (such as for all of the samples of a data series) from NCBI, use prefetch.
 
 Given a set of SRA files listed in a single column in the text file "SraAccList.txt" (e.g. SRR7623010, SRR7623011, etc.), the following command will download the entire set:
 
 {{{
-prefetch -O output_directory sraAccList.txt
+prefetch -O output_directory SRR_Acc_List.txt
 }}}
 
 If you don't specify an output directory, the SRR files will be downloaded to ~/ncbi/ncbi_public/sra (or your configured "Import Path" as described above).  
 
-To get this list of SRR IDs, go the [[https://www.ncbi.nlm.nih.gov/Traces/study/|SRA Run Selector]] and enter a project accession.  Once on a [[https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP000002|project page, go to the "Select" section and click on "Accession List" (or if you want a subset of these, click on "Metadata" in the "Select" section to get a comma separated file, SraRunTable.txt)
+To get this list of SRR IDs, go the [[https://www.ncbi.nlm.nih.gov/Traces/study/|SRA Run Selector]] and enter a project accession.  Once on a [[https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP000002|project page]], go to the "Select" section and click on "Accession List" to get 'SRR_Acc_List.txt' (or if you want a subset of these, click on "Metadata" in the "Select" section to get a comma separated file, 'SraRunTable.txt')