SGSSynteny - Revision history

Agnieszka at 04:20, 18 August 2014

2014-08-18T04:20:26Z

Agnieszka at 02:16, 18 August 2014

2014-08-18T02:16:36Z

Agnieszka at 01:45, 23 June 2014

2014-06-23T01:45:18Z

Agnieszka at 01:40, 23 June 2014

2014-06-23T01:40:07Z

Agnieszka at 01:39, 23 June 2014

2014-06-23T01:39:44Z

Agnieszka at 01:22, 23 June 2014

2014-06-23T01:22:49Z

Agnieszka at 01:22, 23 June 2014

2014-06-23T01:22:05Z

Agnieszka at 01:20, 23 June 2014

2014-06-23T01:20:53Z

Agnieszka at 00:14, 23 June 2014

2014-06-23T00:14:47Z

Agnieszka: Created page with "== What does SGSSynteny depend on? == SGSGeneLoss depends on the following: * [http://www.java.com/en/ Java 1.6] or higher * [http://www.r-project.org/ R/3.1.0] * [http://sourcef..."

2014-06-18T03:06:43Z

Created page with "== What does SGSSynteny depend on? == SGSGeneLoss depends on the following: * [http://www.java.com/en/ Java 1.6] or higher * [http://www.r-project.org/ R/3.1.0] * [http://sourcef..."

New page

== What does SGSSynteny depend on? ==
SGSGeneLoss depends on the following:
* [http://www.java.com/en/ Java 1.6] or higher
* [http://www.r-project.org/ R/3.1.0]
* [http://sourceforge.net/projects/picard/files/picard-tools/ picard-tools]
* [http://ggplot2.org/ ggplot2]

== Download ==
* Latest Version 0.1 (29/04/2014):
** [http://appliedbioinformatics.com.au/download/SGSSynteny.v0.1.tar.gz SGSSynteny.v0.1.tar.gz] should contain
*** four main programs: SGSSynteny.v0.1.jar, graph_synteny.R
*** readme file
*** folder with source code

From now on in this manula SGSSynteny.v0.1.jar and graph_synteny.v0.1.R are referred to as SGSSynteny.jar and graph_synteny.R

To run the programs you have to use full names SGSSynteny.v0.1.jar and graph_synteny.v0.1.R
== How to install? ==
* SGSSynteny.tar.gz
* Unpack SGSSynteny.tar.gz and place SGSSynteny.jar and all the R scripts in chosen directory/directories, for example ./my_synteny
* Move into ./my_synteny and create SGSSynteny_lib directory (on linux: cd ./my_synteny, mkdir SGSSynteny_lib directory)
** The name of the lib directory is the name of the .jar file witout .jar extension + _lib, so if you are using SGSSynteny.v0.1.jar the lib directory is SGSSynteny.v0.1_lib
** The lib directory has to be in '''the same folder as the .jar file'''
* Download picard-tools (SGSSynteny.jar was tested with picard-tools 1.89)
* Place picard-1.89.jar and sam-1.89.jar in ./my_gene_loss/SGSSynteny_lib
* Now you are ready to run SGSGeneLoss

== Input and output files for SGSSynteny.v0.1.jar ==
* Input files:
** Sorted, indexed .bam file with sequencing reads mapped to the reference genome sequence, multiple .bam files can be provided as comma separated list
** Gff3 file with reference genome annotation, has to contain gene, mRNA and exon fields
* Output files
** Result files for each chromosome separately - .cluster files
** File with overall stats - stats.csv

== Command line options for SGSSynteny.jar==

Required:

bamPath - path to bam file, only folder path, do not specify bam file names here, folder has to contain both .bam and .bai files; has to end with “/” or “\”

bamFileList - comma separated list of all the bam files to be used

gffFile - path to .gff3 file, including file name; has to contain at least genes and exons features

outDirPath - directory for the output files; has to end with “/” or “\”

Optional:

expectCov - expected coverage [null]

minFracHor - minimum horizontal coverage required to consider genes as syntenic [0.3]

minCovVer - minimum coverage depth required to consider genes as syntenic [2.0]

chromosomeList - comma separated list of chromosomes, used `all` for all the chromosomes in .bam file [all]

DBepsilon - Eps value for DBSCAN (radius) [26]

DBmin - minPts value for DBSCAN (min cluster size) [24]

genesOrExons - used whole genes or exons for coverage calculations [exons]

mergeDistance - distance (no of genes) separating clusters for them to be merged [30]

esimateMinCovVer - estimate min coverage depth used for clustering based on x points with highest coverage depth, esimateMinCovVer=0.45 – use 45% of points with highest coverage [null]

To see help run: java -jar SGSSynteny.jar help

== Sample command ==
* Please make sure that all your supplied paths end with / or \

== Output files format ==

All the output files are comma separated text files.
*.cluster files - files with results for each chromosome (files use chromosome names as in .bam files)
*stats.csv - file with summary information about all genes

==Plotting results==

Results are visualized using R script.

Two ways of visualization are possible:
*results per chromosome

'''Results per chromosome:'''

What you need:
*script graph_synteny.R
*.clusters files (either basic or extended) with results from SGSSynteny.jar: Chr1.clusters, Chr2.clusters etc.
*directory (location) where files with results from SGSGeneLoss.jar: Chr1.clusters, Chr2.clusters etc. can be found

graph_synteny.R takes one arguments in this order:

1. location of directory where .clusters file are located

Rscript --vanilla graph_synteny.R /home/uqagnieszka/results

== FAQ ==
* If memory consumption is a problem please consider increasing -Xmx or splitting your .bam files

Back to [[Main_Page]]

@@ Line 98: / Line 98: @@
 . output path '''ending with /'''
-  Rscript --vanilla graph_synteny.R /home/uqagnieszka/results 0.4 /home/uqagnieszka/graphs
+  Rscript --vanilla graph_synteny.R /home/uqagnieszka/results 0.4 /home/uqagnieszka/graphs/
 == FAQ ==

← Older revision		Revision as of 01:22, 23 June 2014
Line 82:		Line 82:

	Results are visualized using R script.		Results are visualized using R script.
−
−	~~Two ways of visualization are possible:~~
−	*results per chromosome

	'''Results per chromosome:'''		'''Results per chromosome:'''

← Older revision		Revision as of 01:20, 23 June 2014
Line 71:		Line 71:
	* Please make sure that all your supplied paths end with / or \		* Please make sure that all your supplied paths end with / or \

		+	java -Xmx16g -jar SGSSynteny.jar bamPath=/home/my_bams/ gffFile=/home/references/Bdistachyon_192_gene_exons.gff3 outDirPath=/home/results/ chromosomeList=Bd1,Bd2,Bd3,Bd4,Bd5 bamFileList=my_bam.sorted.bam DBepsilon=30 DBmin=25 expectCov=500 minCovVer=2.0 minFracHor=0.4

	== Output files format ==		== Output files format ==

@@ Line 32: / Line 32: @@
 * Output files
 ** Result files for each chromosome separately - .cluster files
-** File with overall stats - stats.csv
+** File with overall stats - stats.txt
 == Command line options for SGSSynteny.jar==
@@ Line 77: / Line 77: @@
 All the output files are comma separated text files.
 *.cluster files - files with results for each chromosome (files use chromosome names as in .bam files)
-*stats.csv - file with summary information about all genes
+*stats.txt - file with summary information about all genes
 ==Plotting results==

@@ Line 9: / Line 9: @@
 * Latest Version 0.1 (29/04/2014):
 ** [http://appliedbioinformatics.com.au/download/SGSSynteny.v0.1.tar.gz SGSSynteny.v0.1.tar.gz] should contain
-*** two main programs: SGSSynteny.v0.1.jar, graph_synteny.R
+*** two main programs: SGSSynteny.v0.1.jar, graph_synteny.v0.1.R
 *** readme file
 *** folder with source code

@@ Line 88: / Line 88: @@
 *script graph_synteny.R
 *.clusters files (either basic or extended) with results from SGSSynteny.jar: Chr1.clusters, Chr2.clusters etc.
-*directory (location) where files with results from SGSGeneLoss.jar: Chr1.clusters, Chr2.clusters etc. can be found
+*directory (location) where files with results from SGSSynteny.jar: Chr1.clusters, Chr2.clusters etc. can be found
 graph_synteny.R takes three arguments in this order:

@@ Line 24: / Line 24: @@
 * Download picard-tools (SGSSynteny.jar was tested with picard-tools 1.89)
 * Place picard-1.89.jar and sam-1.89.jar in ./my_gene_loss/SGSSynteny_lib
-* Now you are ready to run SGSGeneLoss
+* Now you are ready to run SGSSynteny
 == Input and output files for SGSSynteny.v0.1.jar ==