Changes between Version 12 and Version 13 of SOPs/qc_SRA

Timestamp:

06/22/23 13:42:51 (19 months ago)

Author:

gbell

Comment:

--

SOPs/qc_SRA

@@ -65 +65 @@
 }}} 
 
+If fastq-dump gives you an error like "Failed to call external services." you may need to use the NCBI link to a sralite file to download the sequences in that format first and then convert to fastq.  This can be done with commands like
+
+{{{
+# Download the sralite file
+wget https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/626/SRR1234567/SRR1234567.sralite.1
+
+# Convert sralite to fastq
+fastq-dump --split-files -A SRR1234567 SRR1234567.sralite.1
+}}}
+
 === [=#multiple Downloading and processing multiple NCBI SRA samples] ===