SGSSynteny

What does SGSSynteny depend on?

SGSGeneLoss depends on the following:

• Java 1.6 or higher
• R/3.1.0
• picard-tools
• ggplot2

Download

• Latest Version 0.1 (29/04/2014):
  • 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 SGSSynteny

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 \

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

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 three arguments in this order:

1. location of directory where .clusters file are located

2. lower limit of the Y axis

3. output path ending with /

Rscript --vanilla graph_synteny.R /home/uqagnieszka/results 0.4 /home/uqagnieszka/graphs

FAQ

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

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