Changes

= Build Binary Reference Genome and Word Index =

= Build Binary Reference Genome and Word Index =

First, build a binary version of the genome reference sequence as nucleotides (option: --createReference).  Suppose that NCBI36.fa is a FASTA file which contains nucleotide sequences for all chromosomes.

First, build a binary version of the genome reference sequence as nucleotides (option: --createReference).  Suppose that NCBI36.fa is a FASTA file which contains the nucleotide sequences for all chromosomes.

The command to invoke is:

The command to invoke is:

   karma --createReference --reference NCBI36.fa

   karma --createReference --reference NCBI36.fa

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(To let KARMA map nucleotide space reads, one would use instead ''--createIndex''&nbsp; to create both a binary sequence and the word index files.)<br>

(To let KARMA map nucleotide space reads, one would use instead ''--createIndex''&nbsp; to create both a packed binary sequence file and the word index files.)<br>

Second, one also needs to build color space versions of both the genome reference sequence (option: --createReference) and the word index files (option: --createIndex).&nbsp;  The same nucleotide FASTA file is used.&nbsp;  However, to avoid naming conflicts among the resulting binary files, we suggest appending "CS" to the base file name for clarity.&nbsp;  The command to invoke is:<br>

Second, one also needs to build color space versions of both the genome reference sequence (option: --createReference) and the word index files (option: --createIndex).&nbsp;  The same nucleotide FASTA file is used.&nbsp;  However, to avoid naming conflicts among the resulting binary files, we suggest appending "CS" to the base file name for clarity.&nbsp;  The command to invoke is:<br>

= 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 .csfastq&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; With 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&nbsp; "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 format named &nbsp; "single.sam"&nbsp; derived from the .fastq&nbsp; file name.<br>

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

Multiple input files are also acceptable and will produce multiple .sam output files, e.g.<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&nbsp; file named&nbsp; "pair.1.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>

The mapping results will be stored in a .sam&nbsp; file named&nbsp; "pair.1.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, etc. and write output files&nbsp; "pair.1.sam", "pair.3.sam", etc.<br>

   karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace \

   karma --reference NCBI36.fa --csReference NCBI36CS.fa --colorSpace \

== Minimum read length requirement ==

== Minimum read length requirement ==

Keep in mind that KARMA requires color space reads that are at least twice as long as the index word size plus two (including the leading primer base).&nbsp; (For nucleotide space, the minimum read length is twice the word size.)&nbsp; For example, KARMA uses an index word size of 15 by default, so it will only map color space reads that are 32 base pairs or longer.<br>

Keep in mind that KARMA requires color space reads that are at least twice as long as the index word size plus two (including the leading primer base).&nbsp; (For nucleotide space, the minimum read length is twice the word size.)&nbsp; For example, KARMA uses an index word size of 15 by default, so it will only map color space reads that are 32 colors or longer (including the primer base).<br>

== Auxiliary tools ==

== Auxiliary tools ==