How to generate input wig files for HMMcopy R package?

Question

[monica]

Hello everyone,

I am trying to use the HMMcopy R package for low pass copy number analysis. HMMcopy needs .wig files as input for the analysis. Unfortunately, there is no documentation available about how to obtain these files. Can someone please provide any info about how to generate those wig files for HMMcopy. I have fastq files and i have already generated bam and sam files for those fastq files. Thanks in advance.

Answer 1

[Alex]

Not sure if you figured it out, but I have been looking around on how to do this as well and found this:

http://bioinformatics-ca.github.io/bioinformatics_for_cancer_genomics_mod5_lab_data_prep_2015/

I haven't had the chance to try it yet, but while looking for how to do it I stumbled across your question. I think what we are interested in is towards the bottom of the page for the GC and mapability files. Towards the top is the readCounter for the third wig file needed.

Hope this helps!