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→A Complete Example
= A Complete Example =
= A Complete Example =
A wrap-up message for quick start mapping color space reads.<br>
Building binary genome reference and word index:<br>
Building binary genome reference and word index:<br>
ln -s NCBI36.fa NCBI36CS.fa
ln -s NCBI36.fa NCBI36CS.fa
karma --colorSpace --createReference --createIndex --reference NCBI36CS.fa
karma --colorSpace --createReference --createIndex --reference NCBI36CS.fa
Mapping color space reads:<br>
Mapping color space reads:<br>
karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace single.csfastq
karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace single.csfastq
karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace \
karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace \
--pairedReads pair1.csfastq pair2.csfastq
--pairedReads pair.1.csfastq pair.2.csfastq
The output files are ''single.sam'' and ''pair1.sam'' and they conform SAM specification.
The output files are ''single.sam'' and ''pair.1.sam'' and they conform to the .sam format specification.
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