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, 07:04, 15 November 2009
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| First, we need to build binary reference genome (option: --createReference)<br> | | First, we need to build binary reference genome (option: --createReference)<br> |
− | <ref>To let KARMA map nucleotide space reads, you need to use ``--createIndex''to create the word index file.</ref><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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| == 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<br> twice the size of word plus two (including leading primer) \footnote{For nucleotide space,<br> 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<br> reads that are longer than 32 base pairs.<br> | + | Keep in mind that the requirement of minimum color space read length for KARMA is<br> twice the size of word plus two (including leading primer) <br> |
| + | (For nucleotide space,<br> 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<br> reads that are longer than 32 base pairs.<br> |
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| == Auxiliary tools == | | == Auxiliary tools == |