Changes

We summarize the input data requirements as following:

We summarize the input data requirements as following:

*  A binary conversion of the genome reference sequence as nucleotides (see [[#Build_Binary_Reference_Genome_and_Word_Index|Build Binary Reference Genome and Word Index]]})  

* A binary conversion of the genome reference sequence as nucleotides (see [[#Build_Binary_Reference_Genome_and_Word_Index|Build Binary Reference Genome and Word Index]]})  

*  A binary conversion of the genome reference sequence as colors plus word indices in color space (see [[#Build_Binary_Reference_Genome_and_Word_Index|Build Binary Reference Genome and Word Index]])  

 

*  Color space reads in color space FASTQ format (see [[#Input_file_requirement|Input file requirement]] for a description)  

* A binary conversion of the genome reference sequence as colors plus word indices in color space (see [[#Build_Binary_Reference_Genome_and_Word_Index|Build Binary Reference Genome and Word Index]])  

*  Color space reads longer than a minimum length requirement. (see [[#Minimum_read_length_requirement|Minimum read length requirement]])  

 

*&nbsp; Specify color space parameter when starting KARMA (see [[#Map_Color_Space_Reads|Map Color Space Reads]])<br>

* Color space reads in color space FASTQ format (see [[#Input_file_requirement|Input file requirement]] for a description)  

 

* Color space reads longer than a minimum length requirement. (see [[#Minimum_read_length_requirement|Minimum read length requirement]])  

 

* Specify color space parameter when starting KARMA (see [[#Map_Color_Space_Reads|Map Color Space Reads]])  

Please note the hardware requirements for KARMA are:

Please note the hardware requirements for KARMA are:

<br> We show a complete example demonstrating the whole procedure from building the word index to mapping color space reads in [[#A_Complete_Example|A Complete Example]].

<br> We show a complete example demonstrating the whole procedure from building the word index to mapping color space reads in [[#A_Complete_Example|A Complete Example]].

= Build Binary Reference Genome and Word Index<br> =

= Build Binary Reference Genome and Word Index =

 

The command to invoke is:

The command to invoke is:<br>

   karma --createReference --reference NCBI36.fa

   karma --createReference --reference NCBI36.fa

<br>

<br>

(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>

&nbsp;<br>

&nbsp;<br>

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 \

   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 in 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&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 \

   --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> =

= Additional Information =

== Input file requirement ==

== Input file requirement ==

== 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 ==

The ABI SOLiD platform generates separate FASTA and quality files named&nbsp; XXX.csfasta&nbsp; and&nbsp; XXX\_QV.qual.&nbsp; We provide a script&nbsp; ''solid2csfastq.py''&nbsp; which converts these into a single color space FASTQ file named&nbsp; XXX.csfastq.&nbsp; We believe that a single color space FASTQ file simplifies post processing.<br>

The ABI SOLiD platform generates separate FASTA and quality files named&nbsp; XXX.csfasta&nbsp; and&nbsp; XXX_QV.qual.&nbsp; We provide a script&nbsp; ''solid2csfastq.py''&nbsp; which converts these into a single color space FASTQ file named&nbsp; XXX.csfastq.&nbsp; We believe that a single color space FASTQ file simplifies post processing.<br>

== Choose an appropriate size for word index ==

== Choose an appropriate size for word index ==