Changes

= Map Color Space Reads =

= Map Color Space Reads =

KARMA expects valid color space FASTQ files as input.&nbsp; We often use the suffix .csfastq to distinguish these from nucleotide space reads.&nbsp; For a .csfatq&nbsp; file of single end color space reads named &nbsp; single.csfastq, &nbsp; invoke the command:<br>

KARMA expects valid color space FASTQ files as input.&nbsp; We often use the suffix .csfastq to distinguish these from nucleotide space reads.&nbsp; For a .csfastq&nbsp; file of single end color space reads named &nbsp; single.csfastq, &nbsp; invoke the command:<br>

   karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace single.csfastq

   karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace single.csfastq

This command line specifies both the nucleotide and color space reference sequences (and the word indexes, invisibly).&nbsp; The output will be written to a file in .sam&nbsp; format named "single.sam".<br>

This command line specifies both the nucleotide and color space reference sequences (and the word indexes, invisibly).&nbsp; The output will be written to a file in .sam&nbsp; format named&nbsp; "single.sam".<br>

&nbsp;<br>

Multiple input files are also acceptable, e.g.<br>

Multiple input files are also acceptable, e.g.<br>

   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".&nbsp; Suppose the paired end reads are stored as two files,&nbsp; pair.1.csfastq&nbsp; and&nbsp; pair.2.csfastq.&nbsp; The command to invoke is:<br>

For paired end color space reads, use the option "--pairedReads".&nbsp; Suppose the paired end reads are stored in two files,&nbsp; pair.1.csfastq&nbsp; and&nbsp; pair.2.csfastq.&nbsp; 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.sam", which contains reads from both files.&nbsp; 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>

The mapping results will be stored in a .sam&nbsp; file named&nbsp; "pair.sam", which contains reads from both files.&nbsp; 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 \