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→Map Color Space Reads
karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace \
karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace \
single.1.csfastq single.2.csfastq single.3.csfastq
single.1.csfastq single.2.csfastq single.3.csfastq
For paired end color space reads, use the option "--pairedReads". Suppose the paired end reads are stored in two files, pair.1.csfastq and pair.2.csfastq. The command to invoke is:<br>
For paired end color space reads, use the option "--pairedReads". Suppose the paired end reads are stored in two files, pair.1.csfastq and pair.2.csfastq. The command to invoke is:<br>
karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace \
karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace \
--pairedReads pair.1.csfastq pair.2.csfastq
--pairedReads pair.1.csfastq pair.2.csfastq
The mapping results will be stored in a .sam file named "pair.1.sam", which contains reads from both files. If multiple paired end read files are specified on the command line, KARMA will pair the 1st and 2nd files, 3rd and 4th files and etc.<br>
The mapping results will be stored in a .sam file named "pair.1.sam", which contains reads from both files. If multiple paired end read files are specified on the command line, KARMA will pair the 1st and 2nd files, 3rd and 4th files and etc.<br>
karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace \
karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace \
--pairedReads pair.1.csfastq pair.2.csfastq pair.3.csfastq pair.4.csfastq
--pairedReads pair.1.csfastq pair.2.csfastq pair.3.csfastq pair.4.csfastq
= <br> Additional Information<br> =
= <br> Additional Information<br> =
