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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
1212need to be used, but all chromosomes used in the CNV analysis must be
1313present (with their sizes) in this file.
1414
15- ## Bin definitions The CNV analysis begins with counts of reads in
16- genomic bins. The bins are defined by have roughly equal size, but
15+ ## Bin definitions
16+ The CNV analysis begins with counts of reads in
17+ genomic bins. The bins are defined to have roughly equal size, but
1718account for mappability, so the sizes vary slightly. We use files
1819originally generated by scripts provided along with the publication:
1920```
Original file line number Diff line number Diff line change 11## To test mapping simulated SMURF-seq reads to a small simulated genome
22A simulated reference genome ` ref_sim.fa ` has been indexed with BWA-MEM.
3- ` read_sim.fastq ` contains simulated reads.
3+ ` read_sim.fastq ` contains simulated reads that align to ` ref_sim.fa ` .
44
55## To test mapping simulated reads to the human genome
6- ` read_hg.fastq ` contains simulated reads from the human genome.
6+ ` read_hg.fastq ` contains simulated reads that align to the human genome.
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