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SHRiMP (rmapper) results can vary greatly based upon the input parameters. So please select parameters accordingly.
The input parameters that we typically use with color space data are the following:
rmapper-cs -s 111100111 -n 2 -w 36 -m 100 -i -90 -g -250 -q -250 -e -100 -f -100 -h 2000 -v 1000 in.csfasta ref.fasta
where
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base commands on Fourierseq are:
for color space:
| Code Block |
|---|
gmapper-cs
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and for base space:
| Code Block |
|---|
gmapper-ls
|
The input parameters that we typically use with color space data are the following:
Tip: To view the actual alignments in base space as part of the output file, add -p option (prettyprint).