Download saskSAGE @ sourceforge


Reaping the Benefits of SAGE

From: Methods in Molecular Biology, vol. 406: Plant Bioinformatics: Methods and Protocols. Edited by : D. Edwards © Humana Press Inc., Totowa, NJ 2007.

Stephen J. Robinson1, Justin D. Guenther2, Christopher T. Lewis3, Matthew G. Links1, and Isobel A.P. Parkin1
1Saskatoon Research Centre, Agriculture and Agri-food Canada; 2University of Saskatchewan; 3Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-food Canada;


About saskSAGE

saskSAGE is a set of utilities to use CSAGE to analyze multiple libraries. By combining CSAGE reports from a series of libraries it is possible to perform a chi squared test of variance between SAGE tag and Treatment.

To run saskSAGE you will need to download the core package from sourceforge.


cSAGE and the Serial Analysis of Gene Expression in Arabidopsis thaliana

Christopher T Lewis1, Stephen Robinson2, Tony Kusalik, Isobel AP Parkin
1LewisCT@agr.gc.ca, Agriculture and Agri-food Canada; 2RobinsonS@agr.gc.ca, Agriculture and Agri-food Canada


About CSAGE

CSAGE is a C program to extract sage tags and assign matches to genomics sequence. The mechanism for extracting sage tags is a 5-ary tree with nodes representing A,C,G,T,N, which allows efficient detection of duplicate ditags, and rapid assignment of matches (a tag can be found in the tree in O(m) time, where m is the length of the tag). The functionality is described in more detail in csage_note.

Please note that this description is somewhat out of date -- so some of the functionality differs.

For instance:

The CSAGE suite has been used for a large scale cold tolerance experiment in A. thaliana (manuscript in preparation, contact Steve Robinson). As such the majority of the supporting scripts are geared toward analysis of this data. I will make them available so that others can modify them, or develop their own scripts based on them.


Examples

Reading ../temp/temp//4796756.fasta
Reading ../temp/temp//4796757.fasta
Reading ../temp/temp//4796758.fasta
Reading ../temp/temp//4796759.fasta
 
 
Tree
Tag (id)        Count   dTags   dDitags
   Matching Genes
 
<snip>
TTACACAGAC      (     0)        5       0       0       0.000109
TTACACAGCT      (     0)        1       0       0       0.000022
TTACACAGGA      (     0)        1       0       0       0.000022
TTACACCTGT      (     0)        4       0       0       0.000087
TTACACTAAT      (     0)        1       0       0       0.000022
TTACACTCCA      (     0)        1       0       0       0.000022
TTACACTGGA      (     0)        1       0       0       0.000022
TTACACTTAT      (     0)        1       0       0       0.000022
TTACAGACTT      (     0)        1       0       0       0.000022
TTACAGAGCT      (     0)        2       0       0       0.000043
TTACAGCACA      (     0)        1       0       0       0.000022
TTACAGGCTT      (     0)        1       0       0       0.000022
TTACAGTAGA      (     0)        1       0       0       0.000022
TTACAGTCTT      (     0)        2       0       0       0.000043
TTACAGTGAT      (     0)        1       0       0       0.000022
TTACAGTGTT      (     0)        1       0       0       0.000022
TTACATAAGC      (     0)        1       0       0       0.000022
TTACCAAATC      (     0)        1       0       0       0.000022
TTACCATACC      (     0)        1       0       0       0.000022
TTACCATATC      (     0)        53      0       7       0.001151
TTACCATATG      (     0)        1       0       0       0.000022
TTACCATTGC      (     0)        1       0       0       0.000022
TTACCATTGG      (     0)        4       0       0       0.000087
TTACCCACAC      (     0)        1       0       0       0.000022
TTACCCACTC      (     0)        1       0       0       0.000022
TTACCCATAC      (     0)        1       0       0       0.000022
TTACCCCACA      (     0)        1       0       0       0.000022
TTACCGATAA      (     0)        1       0       0       0.000022
TTACCGTACA      (     0)        1       0       0       0.000022
TTACCTACTT      (     0)        1       0       0       0.000022
TTACCTCAAG      (     0)        1       0       0       0.000022
TTACCTCACC      (     0)        1       0       0       0.000022
TTACCTCCTT      (     0)        30      0       4       0.000652
TTACCTCGTT      (     0)        1       0       0       0.000022
TTACCTCTTC      (     0)        2       0       0       0.000043
TTACCTCTTT      (     0)        1       0       0       0.000022
TTACCTGTAA      (     0)        1       0       0       0.000022
TTACCTTACC      (     0)        4       0       0       0.000087
TTACGAATGA      (     0)        1       0       0       0.000022
TTACGAGGAA      (     0)        3       0       0       0.000065
TTACGATGAA      (     0)        2       0       0       0.000043
TTACGGGATC      (     0)        1       0       0       0.000022
TTACTAAATG      (     0)        11      0       0       0.000239
TTACTAAGGG      (     0)        1       0       0       0.000022
<snip>
 
                  Ditags:  28111
          Invalid Ditags:  1709
        Duplicate Ditags:  3308
      Low Quality Ditags:  0
        Ditags Processed:  23094
 
 Sequence Tags Processed:  46188
    Tags in Exclude File:  0
 
  Sequence Tags Excluded:
         In Exclude File:  0
            Too many N's:  142
          Duplicate Tags:  0
 
     Valid Sequence Tags:  46046
                With N's:  0
                  Unique:  18622
 
        Gene Tags Parsed:  0
                 Matches:  0
 
System time used: 0(s) 110000(us)
User time used: 1(s) 90000(us)

 

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