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Overview for KarmaKarma assembles FASTQ files from Solexa into a set of mapped reads using a genome reference. It does this by first creating a index of the genome reference, then uses portions of the read to index into the reference to find possible matches.The process is time efficient, but uses a lot of memory. For the human genome, you must have 24GB of RAM total. Smaller geomes may be done with smaller amounts of memory. Before using karma to map reads, you must download a reference, then create the karma index it. See our documentation for an example of doing this with the human genome chromosome 22. After the index is created, you can map your FASTQ data against it. To understand what the data should look like, please see our section on fasta and fastq data formats. To run karma, see our section on the various options. |