Changes between Version 46 and Version 47 of SOPs/qc_shortReads

Timestamp:

10/29/18 10:25:21 (6 years ago)

Author:

gbell

Comment:

--

SOPs/qc_shortReads

@@ -64 +64 @@
   from [[https://en.wikipedia.org/wiki/FASTQ_format | Wikipedia's FASTQ page]]
 
+== Preprocessing read files from NCBI SRA ==
+
+**SRA** (for Sequence Read Archive) is a NCBI binary format for short reads.
+
+It's thoroughly described in the [[http://www.ncbi.nlm.nih.gov/books/NBK47528/|SRA Handbook]]
+
+Processing SRA files requires the [[https://ncbi.github.io/sra-tools/|NCBI SRA Toolkit]], which is installed on our systems.
+
+The main command is **fastq-dump <SRA archive file>**, like
+
+''**fastq-dump SRR060751.sra**''
+
+If your reads are paired, by default the #1 and #2 reads will end up concatenated together in the same file.  
+To check if the SRA sample has paired reads or not, go to the [https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=run_browser SRA Run browser], enter the sample ID, and look in the table under "Layout".
+
+To get paired reads into separate files, use a command like
+
+''**fastq-dump --split-files SRR060751.sra**''
+
+You can ask for gzipped output instead of typical fastq:
+
+''**fastq-dump --gzip SRR060751.sra**''
+
+See [[https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump|Converting SRA format data into FASTQ]] for all program options.
+
+Note that a fastq file is about 4-5x larger than its corresponding SRA file.
+
+fastq-dump can be used to download/fetch the SRA file, or you can download (eg. using wget) the SRA file directly and then run fastq-dump to get the fastq file.  Downloading SRA file directly will avoid changing home dir path for large file (see below).
+
+'''Note:''' As of fastq-dump version 2.8.1, running fastq-dump will require the vdb-config to be set up correctly.  By default, downloaded/cache file is copied to the user's home directory, which is likely to run out of space.  Run,
+
+{{{
+vdb-config --restore-defaults
+vdb-config -i #use the GUI to enter a different location.  
+}}}
+
+Manually editing the file, $HOME/.ncbi/user-settings.mkfg, doesn't seem to work.  See [[https://ncbi.github.io/sra-tools/install_config.html | NCBI SRA Installation/Config]].  Other alternatives: i) simply symlink the NCBI directory in your home directory to somewhere else with larger storage, or ii) download the SRA file directly (eg. using wget) before using fastq-dump.
+
+{{{
+#download SRR4090409.sra (e.g. use wget) from SRA and convert to fastq
+fastq-dump SRR4090409.sra
+
+#download SRA file via fastq-dump (important: home directory or vdb-config file must be set up correctly), and convert to fastq
+fastq-dump SRR4090409
+}}}
+
+
 == FastQC ==