Changes between Version 38 and Version 39 of SOPs/mapping

Timestamp:

03/01/17 08:24:20 (8 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -26 +26 @@
 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 fastq-dump.
-
-{{{
-#download SRR4090409.sra (eg. use wget) from SRA and convert to fastq
+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 -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 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 directlry or vdb-config file must be setup correctly), and convert to fastq
+#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
 }}}