SNP Plot::Upload files

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This cgi tool plots genome/chromosomal locations of SNPs (as x axis), to present an overview how pre-grouped SNPs are distributed in the genome. It can also display their associated phenotype values (as y values).

  1. Data within each file upload file suppose to come from one type of analysis which will be represented by one plot color (Here is an example file for you to try it out).
  2. When multiple files are uploaded, they suppose to come from the same TYPE of analysis such that their plots are comparable.

Upload file format

Multi-columns, delimited with spaces or tabs: 
snp_id  value1 value2 value3   ...
With an optional header line*, as in: 
numID   Growth pH     GFreq    ...
16028   32     5.6    5.1e+01  ...
16039   45     4.5    4.1e+02  ...
28931   121    5.1    2.1e+00  ...
21736   98     6.7    4.1e+01  ...
1141    35     5.7    2.1e+00  ...
6334    62     5.3    3.1e+01  ...
7973    77     6.9    1.1e+01  ...
.. .    ..     ...    ......   ...

a) Column 1 is marker ID (numerical)
b) Column 2 etc are phenotype values,
   but only one column will be used
   in the plot (must specify).
c) Header line:
  1.Names for all fields must present,
    Or omitted all together
  2.Each header name should not contain
    any space, Or they may be truncated

Upload your data file(s):

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Choose:

  1. Use absolute values? Yes No
  2. Which column to plot?
  3. SNP id: Gensel ID SNP Name
  4. SNP database:

Note: The order number in which you upload
files will correspond to plot color codes.


To view your sub-set of SNPs in GBrowse, use this GFF Formattor to convert your list of SNP names into a GBrowse-ready GFF file for uploading to GBrowse. 

$Id: snplotz v.1.52 beta Mar 2011
Reference:
Zhi-Liang Hu, Rex Fernando, Dorian Garrick and James M Reecy (2010). SNPlotz: a generic genome plot tool to aid the SNP association studies. BMC Bioinformatics 2010, 11(Suppl 4):P4.

 

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