Changes between Version 7 and Version 8 of SOPs/qc_SRA

Timestamp:

08/26/20 08:54:09 (4 years ago)

Author:

gbell

Comment:

--

SOPs/qc_SRA

@@ -52 +52 @@
 }}}
 
+In the event of problems downloading and converting to fastq.gz all at once, SRA files can be downloaded by navigating through the SRA web site to the sample's "Data access" tab, which provides direct links to the files.  Using this direct path to the SRA file,
+{{{
+# Use 'wget' for download
+wget -O SRR123456.sra https://sra-downloadb/path_to_file/SRR123456/SRR123456.1
+# Convert SRA to fastq.gz
+fastq-dump --split-3 --gzip ./SRR123456.sra
+}}} 
+
 === Downloading and processing multiple NCBI SRA samples ===