search

DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
464 stars 112 forks source link

It's possible that insertions of up to 100 bps ? #359

Open Wenfei-Xian opened 2 years ago

Wenfei-Xian commented 2 years ago

Hi hisat2 team,

      It's possible that allows the maximum length of insertion up to 100 bp ?
parkchanhee commented 2 years ago

You may use the scoring options. The --rfg and --score-min options can be used to control the insertion length, but you can't set the exact maximum insertion length as other penalties also contribute the alignment score.