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Fourierseq - current version: 2.2.1 (updated 11/14/11).
Phylocluster - version: 2.0
User documentation
- To get started using SHRiMP, read through the the SHRiMP documentation.
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The base commands on Fourierseq are:
for color space:
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gmapper-cs
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and for base space:
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gmapper-ls
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The input parameters that we typically use with color space data are the following:
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gmapper-cs -p opp-in -N 4 -1 F3/V3BC17_RNA.csfasta -2 F5/V3BC17_RNA.csfasta /home/scott/Downloads/mouse.rna.fna > bc17.sam 2> bc17.log &
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