search

holstegelab / TREAT

Tandem REpeat Annotation Toolkit (TREAT)
5 stars 0 forks source link

Realignment #2

Open jiadong324 opened 1 month ago

jiadong324 commented 1 month ago

Dear Author,

Thanks for developing this nice tool!

I have some questions regarding to your local assembly steps:

  1. How do you extract the flanking sequence from reference? Is that based on the tandem repeat annotation of that reference genome (eg, HG38).
  2. In your method workflow, the alternative sequence represented in blue is extracted for pairwise alignment. It looks like that the clusters of these sequence is based on the pairwise distance. I am curious about the kernal density estimation, how do you use this to distinguish sequence error.

Looking forward to your comments! Thanks!

TesiNicco commented 2 weeks ago

Hi,

  1. reads from the reference genome are extracted based on the given coordinates in the BED file. No known annotation is involved here.
  2. More details about this procedure are available in the Methods and Supplementary Methods of the paper. Also adding @ansalaza to the conversation as he can probably add

Hope this helps, feel free to reach for further questions Best, Nicco