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, 07:08, 15 November 2009
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| = Build Binary Reference Genome and Word Index<br> = | | = Build Binary Reference Genome and Word Index<br> = |
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− | First, we need to build binary reference genome (option: --createReference)<br> (To let KARMA map nucleotide space reads, you need to use ``--createIndex'' to create the word index file.)<br> | + | First, we need to build binary reference genome (option: --createReference)<br> (To let KARMA map nucleotide space reads, you need to use ''--createIndex'' to create the word index file.)<br> |
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| in nucleotide space. Assume NCBI36.fa is a FASTA file contains sequences of all chromosomes.<br> The command to invoke is:<br> | | in nucleotide space. Assume NCBI36.fa is a FASTA file contains sequences of all chromosomes.<br> The command to invoke is:<br> |
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| <br> | | <br> |
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− | Second, we need to build binary reference genome (option: --createReference) and word index (option: --createIndex)
| + | Second, we need to build binary reference genome (option: --createReference) and word index (option: --createIndex)<br> in color space. The same FASTA file is needed. However, to avoid naming conflicts, we suggest using word "CS" <br> appending to the base file name for clarity. The command to invoke is:<br> |
− | in color space. The same FASTA file is needed. However, to avoid naming conflicts, we suggest using word "CS"
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− | appending to the base file name for clarity. The command to invoke is:
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| ln -s NCBI36.fa NCBI36CS.fa | | ln -s NCBI36.fa NCBI36CS.fa |
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| == Minimum read length requirement == | | == Minimum read length requirement == |
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− | Keep in mind that the requirement of minimum color space read length for KARMA is twice the size of word plus two (including leading primer).<br> (For nucleotide space, the minimum length requirement is twice the word size.)<br> For example, KARMA use word size of 15 by default, so it will try to map color space reads that are longer than 32 base pairs.<br> | + | Keep in mind that the requirement of minimum color space read length for KARMA is twice the size of word plus two (including leading primer).<br> (For nucleotide space, the minimum length requirement is twice the word size.)<br> For example, KARMA use word size of 15 by default, so it will try to map color space reads that are longer than 32 base pairs.<br> |
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| == Auxiliary tools == | | == Auxiliary tools == |