jeffchen2000

I have 500 human WGS samples (depth=20x), and I ran on a cluster with SGE (10 threads, 40GB for each threads with a total 400GB Momory). now 3 days passed,...

heatmap genoCluster_posterior_mean.png lost tracks of original mutation and cell ID?

3

Hi BnpC support genoCluster_posterior_mean.png are only show sequential numbers on x-axis and y-axis, how can I track back to original cell ID and mutation ID? or in other words, are...

how to deal with "too many missing data"

2

Hi BnpC support from your published paper, your tools are best to deal with missing data (more than 20% missing). Now. we have targeted sequencing snDNA samples from FFPE, with...

how can I generate tree file

3

according to the readme, BnpC can generate a output tree file (did I misunderstand?) but when I run this: run_BnpC.py snp.input.txt -tr test.gv I got error like below, it seems...

results not reproducible even random seed '-S' is set

2

when I run shorah.py, I set '-S 100', but the results are not reproducible, (I downloaded and installed shorah in Nov-2018)

overwrite previous results?

1

when I run shorah.py, for some reason the program crashed or I terminated the program, and then I re-run shorah.py (with some parameters changed), will the previous generated intermediate files...

Error in 1:nchr : result would be too long a vector

2

Hi Dariober when I run with unmatched mode (the unmatched bam are merged from 10 un-related normal samples) cnv_facets.R \ -t ./bams/S21-096.bam \ -n merged_normal.bam \ --unmatched \ -vcf vcfs/S21-096.hard-filtered.vcf.gz...

how can I map my cells to an previously generated cluster?

3

Hi there is a publication that has their generated cluster by BnpC, and each cluster associates with a function, now how can I map my data to such an existing...

I am using atacRepsPipe2 for a total 100 samples, it takes days to processing, which is fine though. And I think you have a good pipeline design that if the...