SGSGeneLoss - Revision history

Philippbayer at 10:51, 14 February 2020

2020-02-14T10:51:38Z

2019-04-16T05:12:15Z

‎Plotting results

2016-11-28T03:19:26Z

‎What does SGSGeneLoss depend on?

2014-07-10T05:39:41Z

2014-06-23T01:47:21Z

2014-06-23T00:53:16Z

2014-06-23T00:11:29Z

2014-06-18T03:11:53Z

2014-06-18T03:05:41Z

2014-06-18T02:05:26Z

← Older revision		Revision as of 10:51, 14 February 2020
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	* If memory consumption is a problem please consider increasing -Xmx or splitting your .bam files		* If memory consumption is a problem please consider increasing -Xmx or splitting your .bam files

		+	* Please cite Golicz, A.A., Martinez, P.A., Zander, M., Patel, D.A., Van De Wouw, A.P., Visendi, P., Fitzgerald, T.L. et al. (2015) Gene loss in the fungal canola pathogen Leptosphaeria maculans. Funct. Integr. Genomics, 15, 189–196.

	Back to [[Main_Page]]		Back to [[Main_Page]]

@@ Line 118: / Line 118: @@
 *chrs.csv from SGSGeneLoss.jar run
 *file assigning numeric order to chromosomes (this is done because some chromosomes have complicated names and sorting in ASCII order does not always work) - file should look like this, chromosome names will be replaced by corresponding numbers
-  chrs,no
+  chr,no
   chr1,1
   chr2,2

@@ Line 3: / Line 3: @@
 * [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://sourceforge.net/projects/picard/files/picard-tools/ picard-tools] v1.89 (or directly from https://sourceforge.net/projects/picard/files/picard-tools/1.89/ )
 * [http://ggplot2.org/ ggplot2]
 * [http://www.bioconductor.org/packages/release/bioc/html/ggbio.html ggbio]

@@ Line 71: / Line 71: @@
   chromosomeList=all
-  java -Xmx4g -jar SGSGeneLoss.jar bamPath=/home/uqagnieszka/bams/ bamFileList=arabidopsis.sorted.bam, arabidopsis2.sorted.bam gffFile=/home/gff_files/Athaliana_167_gene_exons.gff3
+  java -Xmx4g -jar SGSGeneLoss.jar bamPath=/home/uqagnieszka/bams/ bamFileList=arabidopsis.sorted.bam,arabidopsis2.sorted.bam gffFile=/home/gff_files/Athaliana_167_gene_exons.gff3
   outDirPath=/home/uqagnieszka/results/ chromosomeList=Chr1,Chr2 minCov=2 lostCutoff=0.05 covCats=0,2,5,10,20 extendedFmt

@@ Line 109: / Line 109: @@
 . output path '''ending with /'''
-  Rscript --vanilla graph_chromosomes.R /home/uqagnieszka/results 0.0 /home/uqagnieszka/graphs
+  Rscript --vanilla graph_chromosomes.R /home/uqagnieszka/results 0.0 /home/uqagnieszka/graphs/
 '''Summary results for all chromosomes, possibly multiple samples:'''

@@ Line 137: / Line 137: @@
 . output file
-  Rscript --vanilla graph_circles.R chrs.csv chrs_order.csv graph1.csv,graph2.csv,graph3.csv out.png
+  Rscript --vanilla graph_circles.R chrs.csv chrs_order.csv graph1.csv,graph2.csv,graph3.csv /home/results/graphs/ out.png
 == FAQ ==

@@ Line 106: / Line 106: @@
 . gene loss cutoff
-  Rscript --vanilla graph_chromosomes.R /home/uqagnieszka/results 0.0
+  Rscript --vanilla graph_chromosomes.R /home/uqagnieszka/results 0.0 /home/uqagnieszka/graphs
 '''Summary results for all chromosomes, possibly multiple samples:'''
@@ Line 121: / Line 123: @@
   chr10,10
-graph_circles.R takes four arguments in this order:
+graph_circles.R takes five arguments in this order:
 . file with chromosome info - chrs.csv from SGSGeneLoss.jar run
@@ Line 131: / Line 133: @@
 first file in the list is the innermost circle, so if you have graph1.csv,graph2.csv,graph3.csv, order of circles will reflect order of files, starting from the inside
-. output file
+. Output path '''ending with /'''
   Rscript --vanilla graph_circles.R chrs.csv chrs_order.csv graph1.csv,graph2.csv,graph3.csv out.png

@@ Line 23: / Line 23: @@
 * Move into ./my_geneloss and create SGSGeneLoss_lib directory (on linux: cd ./my_geneloss, mkdir SGSGeneLoss_lib directory)
 ** The name of the lib directory is the name of the .jar file without .jar extension + _lib, so if you are using SGSGeneLoss.v0.1.jar the lib directory is: SGSGeneLoss.v0.1_lib
-** The lib directory has to be in the same folder as the .jar file
+** The lib directory has to be in '''the same folder as the .jar file'''
 * Download picard-tools (SGSGeneLoss was tested with picard-tools 1.89)
 * Place picard-1.89.jar and sam-1.89.jar in ./my_geneloss/SGSGeneLoss_lib

@@ Line 112: / Line 112: @@
 What you need:
 *script graph_circles.R
-*graph.txt from SGSGeneLoss.jar run
+*graph.csv from SGSGeneLoss.jar run
-*chrs.txt from SGSGeneLoss.jar run
+*chrs.csv from SGSGeneLoss.jar run
 *file assigning numeric order to chromosomes (this is done because some chromosomes have complicated names and sorting in ASCII order does not always work) - file should look like this, chromosome names will be replaced by corresponding numbers
   chrs,no