安裝中文字典英文字典辭典工具!
安裝中文字典英文字典辭典工具!
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- sequenza - chromosomes are removed when I run sequenza. extract.
What is in the file: out_PAAD_small seqz gz? Try and see if all the chromosomes are in the file I tried sequenza on the test data set and it worked fine, so it is possible that there is a problem with the input
- map error sequenza from Strelka vcf. somatic. snvs in python 3. 8 and . . .
p s when I read source code, vcf py "sequenza-utils" uses Tier 2 allele depth from Strelka 2 pipeline Is it reasonable?
- Question about Copy-Number Data produced using Sequenza
The Sequenza data tells me a "seg mean" value for pretty much every mutation (once I matched the coordinates from the two output files) What I'm trying to figure out is how I can combine these values to filter my list to only diploid mutations which haven't been amplified or deleted
- Use Sequenza output to run GISTIC2 - biostars
From Sequenza output, there are following 13 columns, I am wondering which one I should use for GISTIC2 to calculate Set CN? "chromosome" "start pos" "end pos" "Bf" "N BAF" "sd BAF" "depth ratio" "N ratio" "sd ratio" "CNt" "A" "B" "LPP"
- Problem while working with sequenza - Chromosomes out of order - Biostar: S
Hi, I'm trying to work with sequenza in order to calculate HRD score of a sample using WES data When I run sequenza, I get a message saying that "chromosomes are out of order", and I don't know how to solve it, so if you could help me I would really appreciate it
- Interpreting ASCAT CNV output - Biostar: S
@A I am using a similar approach, but I used Sequenza tool While preparing gistic2 input, I defined Seg CN = log2(2 × depth ratio) – 1 Do you think, I should divide the total copy number of each locus for each sample by the ploidy of that sample?
- converting varscan2 output to sequenza - Biostar: S
Hi I'm trying to run a sequenza with the output of varscan2 I used VarScan version of 2 4 3 and put into sequenza but I got an error message "Error in data frame(chromosome = as character(varscan somatic$chrom), : arguments imply differing number of rows: 0, 1"
- Some questions of Sequenza using WGS - biostars
I am doing research using sequenza It is very useful and powerful tools But, I have some questions of sequenza using WGS Using sequenza extract, it has some error in R I used this code: library(sequenza) library(copy number) data file=paste0("12TB seqz edit gz") test = sequenza extract(data file, verbose=FALSE, assembly="hg19") Error
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