Changes between Version 52 and Version 53 of SOPs/qc_shortReads

Timestamp:

08/19/20 11:49:26 (4 years ago)

Author:

byuan

Comment:

--

SOPs/qc_shortReads

@@ -114 +114 @@
 }}}
 
-In order to '''download a list of SRA files''' from NCBI, it is convenient to use prefetch.  Given a set of SRA files listed in a single column in the text file "sraFileList.txt" (e.g. SRR7623010, SRR7623011, etc.), the following command will download the entire set:
-
-{{{
-prefetch --option-file sraFileList.txt
+In order to '''download a list of SRA files''' from NCBI, it is convenient to use prefetch. 
+
+As mentioned in [[https://www.ncbi.nlm.nih.gov/sra/docs/sradownload/| SRA website ]], you can download list of Run accessions from search results page ([[https://www.ncbi.nlm.nih.gov/sra/?term=cancer |- Example offsite image]]) - select Runs of interest by clicking on the checkboxes, click on "Send To", "file", and select "Accession List" in the drop-down menu.
+
+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 --option-file sraAccList.txt
 }}}
 
@@ -124 +128 @@
 /repository/user/main/public/root = "/destination/for/big/storage/here"
 }}}
+
+or point to the destination folder with -O 
+
+
+Download Metadata:
+When in your GEO series page, click on SRA link -> click on "Send to" on the top of the page -> check the "File" radiobutton, and select "RunInfo" in pull-down menu. This will generate a tabular SraRunInfo.csv file with metadata available for each Run.
+
 
 == FastQC ==