Closed Coaxecva closed 6 months ago
Hi, The LogR is noisy. which mode of the ASCAT are you using? Do you have normal control or use the tumor only mode?
I followed the guidance outlined here: https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WES.
I believe I used normal control. The code is below:
`library(ASCAT)
args<-commandArgs(TRUE)
tumor <- args[1] normal <- args[2]
bname_tumor <- sub('\.bam$', '', basename(tumor)) bname_normal <- sub('\.bam$', '', basename(normal))
ascat.prepareHTS( tumourseqfile = tumor, normalseqfile = normal, tumourname = bname_tumor, normalname = bname_normal, allelecounter_exe = "alleleCounter", alleles.prefix = "/.../ASCAT/G1000_allelesAll_hg38/G1000_alleles_hg38_chr", loci.prefix = "/.../ASCAT/G1000_lociAll_hg38/G1000_loci_hg38_chr", gender = "XY", genomeVersion = "hg38", nthreads = 8, tumourLogR_file = paste(bname_tumor,"TumorLogR.txt",sep=""), tumourBAF_file = paste(bname_tumor,"TumorBAF.txt",sep=""), normalLogR_file = paste(bname_normal,"GermlineLogR.txt",sep=""), normalBAF_file = paste(bname_normal,"GermlineBAF.txt",sep=""))
ascat.bc = ascat.loadData(Tumor_LogR_file = paste(bname_tumor,"TumorLogR.txt",sep=""), Tumor_BAF_file = paste(bname_tumor,"TumorBAF.txt",sep=""), Germline_LogR_file = paste(bname_normal,"GermlineLogR.txt",sep=""), Germline_BAF_file = paste(bname_normal,"GermlineBAF.txt",sep=""), gender = 'XY', genomeVersion = "hg38") ascat.plotRawData(ascat.bc, img.prefix = "Beforecorrection") ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = "/.../ASCAT/GC_G1000_hg38.txt", replictimingfile = "/.../ASCAT/RT_G1000_hg38.txt") ascat.plotRawData(ascat.bc, img.prefix = "Aftercorrection") ascat.bc = ascat.aspcf(ascat.bc) ascat.plotSegmentedData(ascat.bc) ascat.output = ascat.runAscat(ascat.bc, gamma=1, write_segments = T)`
Based on your output, the logR is very noisy, which results in the failure of the next segmentation. You can tell that from the third jumping and noisy segment plots of logR. You may need to check that your data quality, like the coverage, and also, whether your tumor and normal are matched pair. Thanks.
Hi,
I faced a situation akin to a previously reported issue. ASCAT was unable to ascertain an optimal ploidy.
How can I ensure that the sample is suitable for ploidy calculation? Are there additional factors I should examine to understand the underlying issues?
Thank you in advance,
Coax
After_correction
LogR
BAF
LogR
BAF
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