lindenb
commented
4 years ago Hi
Have you planned to add an option to do this in the near future?
no :-)
know an alternative might be to use a combination of pcrclipreads
yes, that's what I would have suggested.
but samjs may be more straightforward to do this.
no, I don't think so.
MaestSi
Dear Pierre, I am using your tool samjs as you suggested in this post. Similarly to the person who opened the post, I would like to keep only the portion of long-reads overlapping the bed file. In particular, I have a primary and many supplementary alignments mapping to a region of interest, and I would like to extract all those reads portions. Have you planned to add an option to do this in the near future? I know an alternative might be to use a combination of pcrclipreads and samextractclip, but samjs may be more straightforward to do this. Thanks in advance, Simone