Created
February 27, 2018 22:06
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Comparing two exome sequencing capture kits
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| url1 <- "https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nexterarapidcapture/nexterarapidcapture_exome_targetedregions.bed" | |
| url2 <- "https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nexterarapidcapture/nexterarapidcapture_expandedexome_targetedregions.bed" | |
| library(rtracklayer) | |
| rapidgr <- import(url1, genome="hg19") | |
| expandedgr <- import(url2, genome="hg19") | |
| library(GenomicRanges) | |
| table(countOverlaps(rapidgr, expandedgr)) | |
| rapidgr <- rapidgr[countOverlaps(rapidgr, expandedgr) == 6] | |
| expandedgr <- expandedgr[expandedgr %over% rapidgr] | |
| session <- browserSession("UCSC") | |
| track(session, "rapid") <- rapidgr | |
| track(session, "expanded") <- expandedgr | |
| browserView(session, range=rapidgr*0.75) |
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