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lines changed Original file line number Diff line number Diff line change @@ -12,8 +12,9 @@ for the size of the chromosome. Not all chromosomes named in this file
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need to be used, but all chromosomes used in the CNV analysis must be
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present (with their sizes) in this file.
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- ## Bin definitions The CNV analysis begins with counts of reads in
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- genomic bins. The bins are defined by have roughly equal size, but
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+ ## Bin definitions
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+ The CNV analysis begins with counts of reads in
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+ genomic bins. The bins are defined to have roughly equal size, but
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account for mappability, so the sizes vary slightly. We use files
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originally generated by scripts provided along with the publication:
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```
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## To test mapping simulated SMURF-seq reads to a small simulated genome
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A simulated reference genome ` ref_sim.fa ` has been indexed with BWA-MEM.
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- ` read_sim.fastq ` contains simulated reads.
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+ ` read_sim.fastq ` contains simulated reads that align to ` ref_sim.fa ` .
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## To test mapping simulated reads to the human genome
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- ` read_hg.fastq ` contains simulated reads from the human genome.
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+ ` read_hg.fastq ` contains simulated reads that align to the human genome.
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