Changes between Version 11 and Version 12 of SOPs/qc_SRA

Timestamp:

10/20/20 11:04:08 (4 years ago)

Author:

gbell

Comment:

--

SOPs/qc_SRA

@@ -77 +77 @@
 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" 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' and create your own 'SRR_Acc_List.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' and create your own 'SRR_Acc_List.txt').  Or you can go to the [[https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=search_seq_name|Downloading SRA data]] page, enter a list of SRX (experimental accession) IDs, and get a list of SRR (sample) accessions for 'SRR_Acc_List.txt'.
 
 The 'prefetch' command will provide you with a set of SRA files which then need to be converted to fastq.gz.  One way to do this on the set of SRA files is