mcfrith / dnarrange Goto Github PK

Hi,

I just read your recently published paper "A pipeline for complete characterization of complex germline rearrangements from long DNA reads" and I found it very interesting, thank you for this work. I am trying to go through your pipeline here and here. I have a couple of questions regarding step 1:

• I have installed the latest version of last (v1080) but I cannot find the binary for last-train which is used in your pipeline to compute indels and substitutions rate. As a measure of precaution, I also download v983 but again, all last binaries are there except last-train. I just found it, it is in a different folder, sorry about that.

• On this page, you describe how to repeat-mask the reference genome. I download the reference genome hg38.analysisSet as you mentioned in Appendix A and it seems to me that the chromosomes have already been repeat-masked. Do I still need to do the repeat-masking procedure in that case?

• I see that your repository for dnarrange (here) contains only binaries. Will you also make the code available?

Thank you for help and time.
Guillaume