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Line 38: − KARMA takes valid color space FASTQ files inputs.<br> We usually use suffix .csfastq to distinguish it from nucleotide space reads.<br> For single end color space read, we can invoke command:<br>+ − + + + − single1.csfastq single2.csfastq single3.csfastq + − − <br> − For paired end color space reads, option "--pairedReads" is requires.<br> Suppose the paired end reads are stored in file, pair1.csfastq and pair2.csfastq.<br> The command to invoke is:<br>+ − + − Mapping results are store in a SAM file named "pair1.sam", which contains reads from both files.<br> <br> Similarly multiple paired end reads files can be specified in command line, and KARMA will pair 1st and 2rd file, 3rd and 4th file and etc.<br>+ − +
→Map Color Space Reads
= Map Color Space Reads =
= Map Color Space Reads =
KARMA expects valid color space FASTQ files as input. We often use the suffix .csfastq to distinguish these from nucleotide space reads. For a .csfatq file of single end color space reads named single.csfastq, invoke the command:<br>
karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace single.csfastq
karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace single.csfastq
Mapping results are store in a SAM file named "single.sam".<br> <br> Multiple input files are also acceptable, e.g.<br>
This command line specifies both the nucleotide and color space reference sequences (and the word indexes, invisibly). The output will be written to a file in .sam format named "single.sam".<br>
Multiple input files are also acceptable, e.g.<br>
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
For paired end color space reads, use the option "--pairedReads". Suppose the paired end reads are stored as 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 pair1.csfastq pair2.csfastq
--pairedReads pair.1.csfastq pair.2.csfastq
The mapping results will be stored in a SAM file named "pair.sam", which contains reads from both files. If multiple paired end reads 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 pair1.csfastq pair2.csfastq pair3.csfastq pair4.csfastq
--pairedReads pair.1.csfastq pair.2.csfastq pair.3.csfastq pair.4.csfastq
= <br> Additional Information<br> =
= <br> Additional Information<br> =
