Burçak Otlu

icon indicating a website link https://sites.google.com/cloud.ucsd.edu/the-alexandrov-lab/ icon indicating an email [email protected]

icon company University of California San Diego icon location San Diego, CA, USA icon location I like coding in java, python, and R. I'm working on bioinformatics, computational biology and statistical genomics. I like working with trees and graphs.

Results 7 comments of Burçak Otlu

For simulating mutations in chrY, I need whether number of mutations in chrY is greater than zero using SPMG.

Dear @mdbarnesUCSD, Thanks for the explanation. I was checking those files. I have the latest versions of the tools: SigProfilerMatrixGenerator 1.2.30 and SigProfilerSimulator 1.1.6 Chrom-based files were created without "chrom_based=True"...

For simulating mutations in chrY, I need whether number of mutations in chrY is greater than zero using SPMG.

Dear all, I deleted all the directories and made a clean run with the following call: **matrices = matGen.SigProfilerMatrixGeneratorFunc(jobname, genome, inputDir, plot=False, seqInfo=True, chrom_based=False)** DEBUG mutation_types: ['SBS', 'DBS', 'ID'] DEBUG...

For simulating mutations in chrY, I need whether number of mutations in chrY is greater than zero using SPMG.

If SPMG is run with seqInfo=True and chrom_based=True, are the matrices returned by SPMG have keys for all given mutation types such as SBS, DBS, and ID mutation types in...

For simulating mutations in chrY, I need whether number of mutations in chrY is greater than zero using SPMG.

I have tested [v1.2.31 release](https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/releases/tag/v1.2.31), and it works correctly on my side—many thanks.

For simulating mutations in chrY, I need whether number of mutations in chrY is greater than zero using SPMG.

When we run the matrix generator with seqInfo=True and chrom_based=True, the all files are not created. e.g., under output/DBS/ there are files named "jobname.DBS78.all.chr1" up to "jobname.DBS78.all.chrY" but there is...

For simulating mutations in chrY, I need whether number of mutations in chrY is greater than zero using SPMG.

It would be great to get non-chromosome based matrices (*.all files) when SPMG is called with chrom_based = True. Path to these matrices are required for SigProfilerAssignment calls in case...

DOC: min_itemsize for HDFStore append for encoded strings

I'm trying to store dataframes in a store. In the first dataframe, I have a 'chrNumber' column of 1 in that column. In the further dataframes, I have a 'chrNumber'...