morrislab / tracksig Goto Github PK

Hello:

I can run tracksig for each samples and can get the figures. Do you know how to get the similar figure like in PCAWG heterogeneity paper (Proportion of mutation for subclone/clone vs Activity Change %). Can you explain what is the “Activity Change” and how to get the data for this figure. Thanks.

I've been altering the bin size for the test example that is presented in the usage section of the README (not using simulated input). I changed 100 to a variable in the make_counts.sh, compute_mutational_signatures.R and helper_functions.R scripts but for bin sizes larger that 100 I am getting exposures larger than 100 (see plot attached, this is for bin size 150). Do you have any idea why this might be happening?

This error occurred after generating all bootstrap files

Error in names(group.colors) <- c(popular, setdiff(colnames(alex), popular)) : 
  'names' attribute [36] must be the same length as the vector [30]
Calls: compute_errorbars_for_all_examples ... plot_signatures_real_scale -> get_group_colors_all_sigs
Execution halted

Hey, I am trying to install and try Tracksig. I am having trouble installing Bio::DB::Fasta module. I have created a conda enviornment and trying to install it via cpan, via cpan Bio::DB::Fasta. I tried many times but I keep getting

Can't locate Bio/DB/Fasta.pm in @INC (you may need to install the Bio::DB::Fasta module)

I wonder if you have any recommendation to make it possible for me to install it?

Hi!

I tried adding signatures 31-35 to the alexsignatures.txt, alexsignatures_w_header.csv, and to the active sig file. I am basically only interested in signature 35 of those but it doesn't seem to look for signature 35 when I run the code. Any ideas on how I can get it to check?

Thanks,
Michael

Quick question here regarding extending TrackSig beyond the hg19 reference build. In src/getMutationTypes.pl, line 16 has the explicit delineation of using hg19:
my %fastaHandles = ("path" => "annotation/hg19/");

My question is, could other reference files be used, like hg38, with the corresponding set of chromosomes used, and simple alteration of line 16? Would this result in any meaningful change of performance in TrackSig? Or is TrackSig meant to be used only with hg19-aligned genomes?