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, 06:56, 15 November 2009
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| * Binary reference genome and word index in color space (see \ref{sec:2}) | | * Binary reference genome and word index in color space (see \ref{sec:2}) |
| * Color space reads in valid color space FASTQ format (see [[#Input file requirement|Input file requirement]] for file specification) | | * Color space reads in valid color space FASTQ format (see [[#Input file requirement|Input file requirement]] for file specification) |
− | * Color space reads are longer than minimum length requirement. (see \ref{sec:4.2}) | + | * Color space reads are longer than minimum length requirement. (see [[#Minimum read length requirement|Minimum read length requirement]]) |
| * Specify color space parameter when starting KARMA (see \ref{sec:3})<br> | | * Specify color space parameter when starting KARMA (see \ref{sec:3})<br> |
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| karma --colorSpace --createReference --createIndex --reference NCBI36CS.fa | | karma --colorSpace --createReference --createIndex --reference NCBI36CS.fa |
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− | An important parameter is the size of words for indexing.<br> We recommand 15 (default value) for human reference genome.<br> Specifiy ``--wordSize N`` if you like to use $N$ as word size.<br> Typically you will observe performance change (see \ref{sec:4.4} for more discussion).<br> <br> <br> Note, multiple chromosomes are supported.<br> In current version, KARMA can take one FASTA file which contains sequences of all chromosomes.<br> | + | An important parameter is the size of words for indexing.<br> We recommand 15 (default value) for human reference genome.<br> Specifiy ``--wordSize N`` if you like to use $N$ as word size.<br> Typically you will observe performance change (see [[#Choose an appropriate size for word index|Choose an appropriate size for word index]] for more discussion).<br> <br> <br> Note, multiple chromosomes are supported.<br> In current version, KARMA can take one FASTA file which contains sequences of all chromosomes.<br> |
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