Sra-tools - Revision history

Rf at 17:53, 29 March 2017

2017-03-29T17:53:07Z

2016-11-16T17:43:52Z

2016-11-16T17:42:47Z

2016-11-16T17:41:49Z

2016-11-16T17:40:30Z

2016-10-14T15:18:37Z

2016-10-14T15:11:28Z

2016-08-29T14:44:53Z

2016-08-04T17:41:22Z

2016-08-04T17:36:58Z

← Older revision		Revision as of 17:53, 29 March 2017
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	Often when an assembly or sequencing project is run, the authors will upload the raw data to SRA.		Often when an assembly or sequencing project is run, the authors will upload the raw data to SRA.
		+
		+	Its principle tool is '''fastq-dump'''.
		+
		+	= Quick Tips =
		+
		+	Always use
		+	fastq-dump --gzip --split-3 <RUN_NAME>
		+
		+	To download the short read run. Without the options it will just download a single FASTQ file, or a SRA file. The FASTQ file is not easily split if available locally, that's why it's best to specifiy these options in the download stage.

	Due to its size the reads are archived in SRA files which are a special form of compression. The '''fastq-dump''' tool from this module is used to inflate this file format.		Due to its size the reads are archived in SRA files which are a special form of compression. The '''fastq-dump''' tool from this module is used to inflate this file format.

@@ Line 184: / Line 184: @@
 * [https://www.biostars.org/p/111040/ biostars post on downloading from GEO]
-* [https://edwards.sdsu.edu/research/fastq-dump Scott Edwards talks about fastq-dump]
+* [https://edwards.sdsu.edu/research/fastq-dump Rob Edwards talks about fastq-dump]
 = Installation notes =

@@ Line 184: / Line 184: @@
 * [https://www.biostars.org/p/111040/ biostars post on downloading from GEO]
 = Installation notes =
@@ Line 189: / Line 190: @@
 * AsperaConnect is also installed and its module loaded by default when loading the sra-tools module.
 * To making using prefetch easier, there is a environment variable called $ASPERASTR that can be used.

← Older revision		Revision as of 17:41, 16 November 2016
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	* AsperaConnect is also installed and its module loaded by default when loading the sra-tools module.		* AsperaConnect is also installed and its module loaded by default when loading the sra-tools module.
	* To making using prefetch easier, there is a environment variable called $ASPERASTR that can be used.		* To making using prefetch easier, there is a environment variable called $ASPERASTR that can be used.
		+
		+	= Links =
		+
		+	* [https://edwards.sdsu.edu/research/fastq-dump Scott Edwards talks about fastq-dump]

@@ Line 21: / Line 21: @@
 == simple wget method ==
-If you have the name of a run, say, SRR1735578, you can use wget to download my recontstructing the ftp URL.
+This can be often be useful when the remote retrieval part of the '''fastq-dump''' is not obtaining the short reads properly.
   wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR173/SRR1735578/SRR1735578.sra

@@ Line 7: / Line 7: @@
 Due to its size the reads are archived in SRA files which are a special form of compression. The '''fastq-dump''' tool from this module is used to inflate this file format.
-As usual with any NCBI tool, the configuration can be complicated. On top of it some options do not seem to work
+As usual with any NCBI tool, the configuration can be complicated. Often, tim ewill be spent geting SRX numbers (experiments to correspond with the SRR's (runs).
-Asperaconnect is a an IBM tool which is able to be closely integrated with SRA. NOTE: Asperaconnect seems only to be installable on a per-user basis.
+'''NB''': It is important to know whether they are single (often forward) or pair-end reads. The '''-split-files''' and '''--split-3''' options will not generate reverse read files in such conditions, naturally enough.
 = Usage =

@@ Line 1: / Line 1: @@
 = Introduction =
-SRA is the NCBI Short Read Archive. It is an immense database of short reads from a large number of project from research intitutions around the world.
+SRA is the NCBI Short Read Archive. It is an immense database of short reads from a large number of project from research intitutions around the world who decide to upload to the NCBI.
 Often when an assembly or sequencing project is run, the authors will upload the raw data to SRA.
-Due to its sie the reads are archived in SRA files whihc are a special form of compression. The '''fastq-dump''' tool from this module is used to do this.
+Due to its size the reads are archived in SRA files which are a special form of compression. The '''fastq-dump''' tool from this module is used to inflate this file format.
 Asperaconnect is a an IBM tool which is able to be closely integrated with SRA. NOTE: Asperaconnect seems only to be installable on a per-user basis.

@@ Line 39: / Line 39: @@
   fastq-dump --gzip --split-3 SRR493366.sra
-This will output the dataset as a compressed gzip file, and the '''--split-3''' option will arrange the paired reads in the canonical manner: two fastq files set up with '''_1''' for right-moving reads and ''''_2''', for their lef-moving counterparts
+This will output the dataset as a compressed gzip file, and the '''--split-3''' option will arrange the paired reads in the canonical manner: two fastq files set up with '''_1''' for right-moving reads and ''''_2''', for their left-moving counterparts. Note that in his case, the short reads seems to be a downloaded file. Well, fastq-dump will also fetch from remote servers with only the run name. As in:
 =="--help" output==

← Older revision		Revision as of 17:36, 4 August 2016
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	module load sra-tools		module load sra-tools
		+
		+	== simple wget method ==
		+
		+	If you have the name of a run, say, SRR1735578, you can use wget to download my recontstructing the ftp URL.
		+
		+

	== fastq-dump ==		== fastq-dump ==