Changes between Version 36 and Version 37 of SOPs/mapping

Timestamp:

02/28/17 16:03:54 (8 years ago)

Author:

thiruvil

Comment:

--

SOPs/mapping

@@ -24 +24 @@
 Note that a fastq file is about 4-5x larger than its corresponding SRA file.
 
-As of fastq-dump version 2.8.1, running fastq-dump will require the vdb-config to be setup correctly.  By default, downloaded/cache file is copied to the user home director which is likely to run out of space.  Run ''vdb-config -i'' and 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]]
+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).
+
+As of fastq-dump version 2.8.1, running fastq-dump will require the vdb-config to be setup correctly.  By default, downloaded/cache file is copied to the user home director which is likely to run out of space.  Run ''vdb-config -i'' and 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 SRA file directly (eg. using wget) before using wget.
+
+{{{
+#download SRR4090409.sra (eg. use wget) from SRA and convert to fastq
+fastq-dump SRR4090409.sra
+
+#download SRA file via fastq-dump (important: home directlry or vdb-config file must be setup correctly), and convert to fastq
+fastq-dump SRR4090409
+}}}
 
 == Mapping short reads ==