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README.md

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@@ -57,13 +57,14 @@ The reference genome should be a single whole FASTA file containg all chromosome
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* `hg38/GRch38`: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz Remember to decompress hg38.fa.gz since it is gzipped and is not supported currently.
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## Target file
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The target file is a bed file giving the MSI locuses. VisualMSI will compute the target MSI locus using the center between the start and the end position. To add a MSI target locus at `chr:pos`, you can add a row with values (chr, pos-100, pos+100, name). You can see the example from targets/msi.bed:
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The target file is a bed file giving the MSI locuses. To add a MSI target locus at `chr:position`, you can add a row with values (chrom, position, name). You can see the example from targets/msi.bed:
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```TSV
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chr4 55588112 55608311 BAT25
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chr2 47631460 47651659 BAT26
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chr14 23642268 23662467 NR-21
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chr11 102183409 102203608 NR-27
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chr2 95839262 95859461 NR-24
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#CHROM POSITION NAME
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chr4 55598216 BAT25
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chr2 47641568 BAT26
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chr14 23652365 NR-21
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chr11 102193518 NR-27
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chr2 95849372 NR-24
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```
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Please note that this bed file is based on hg19 coordination.
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