NTAP Installation

NTAP is composed by a bunch of Perl and R scripts. For that both Perl and R are availabe on all mainstream operating systems including Linux, Windows and Mac OS X, NTAP can be used in either of the systems also. Nevertheless, we recommend you to use it under Linux for best performance. The pre-required software/packages are available freely at following addresses:

  
  R package: http://www.r-project.org/ 
  
  limma package for R from bioconductor project: http://www.bioconductor.org/ 
  
  Perl: http://www.activestate.com/
  
  * If you want to use NTAP under Windows, GhostScript is required to make bitmap format plots: http://ghostscript.com
  

Once you have all the above softwares installed successfully, you can download NTAP from our website and extract it into your working directory. Please don't change the structure of the sub directories automatically generated. Put your raw NimbleGen and genome data into corresponding directories before running the scripts. Please find information in the Usage page for how to use NTAP.

  NTAP - NimbleGen Tiling Array Analysis Package.

After you have installed pre-required softwares and packages (http://ntap.cbi.pku.edu.cn/install.php),
please run "batch.sh" to analysis the sample file included in this pakage. An log file named "nohup.out"
will be created automatically.
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Results will be generated under following two directories:
./plots/ - contain all the figures generated
./results/ - contain the data generated, GFF format files for Generic GBrowse to visualize.


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Sample Files:

./data/ - This directory contains sample data from Li, X., et al. (2008), The Plant cell, 20, 259-276.
3 samples and each sample with 2 biological replicates:
57991_cy3.mrg
57991_cy5.mrg
59178_cy3.mrg
59178_cy5.mrg
59302_cy3.mrg
59302_cy5.mrg

Genes.coords - Genes coordination on the chromosome, please prepare your coords file according to the format.
Ids.txt - Records of all the chip data IDs, corresponding to above files, please change the IDs according to your own data files.
OligoSites.txt - The oligos position on the chromosomes.
SpotTypes.txt - Mark different kinds of spots on the array out. For examples, some bright spots for calibration.

./genelists/ - This directory contains the user-defined gene groups to compare with each other.
1kb-2kb.gid
gt2kb.gid
less1kb.gid


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R scripts:
ntap.R
run.R
sliding_window.R


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Shell & Perl scriptions under ./bin/ directory:
checkdir.sh
clean.sh
compile.sh
pvalue2rec.pl
tigr_xml_cds_coords.pl


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Perl Modules under ./lib/ directory:
Evidence.pm
Gene_obj.pm
Gene_ontology.pm
Model_obj.pm
NimbleGen_Parser.pm
Nuc_translator.pm
TIGR_XML_parser.pm *
txtModelsParser.pm

*: Credit to the TIGR sequencing group.