Hi all,
I have read posts of heat map creation but I am one step prior --
Here is what I am trying to do and wonder if you have any tips?
We are trying to map sequence reads from tumors to viral genomes.
Example input file :
111 abc
111 sdf
111 xyz
1079 abc
1079 xyz
1079 xyz
5576 abc
5576 sdf
5576 sdf
How may xyz's are there for 1079 and 111? How many abc's, etc?
How many times did reads from sample (1079) align to virus xyz.
In some cases there are thousands per virus in a give sample, sometimes one.
The original file (two columns by tens of thousands of rows; 20 MB) is
text file (tab delimited).
Output file:
abc sdf xyz
111 1 1 1
1079 1 0 2
5576 1 2 0
Or, other ways to generate this data so I can then use it for heat map
creation?
Thanks for any help you may have,
rtsweeney
palo alto, ca
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