samclip min clip length

Hi Dr Seemann, Could you add an option --min NUM Minimum clip length required to samclip? or a cutoff of ratio between mapped and unmapped length.

Edison

Sep 06 '18 09:09 Edison2021

@Edison2021 i do not understand exactly what you mean? is this different to the existing --max option?

Sep 15 '19 23:09 tseemann

Hi Dr Seemann, I would like to extract clipped fragments under defined length. For instance, the clipped fragments are must between 50-100bp. So, options such as --min Minimum clip length to allow or --R ratio between mapped and unmapped length would be helpful.

Best Edison

Sep 16 '19 00:09 Edison2021

So you want the SAM lines where more than 50bp is soft-clipped, or less than 100bp is soft-clipped?

Would samclip --max ?? | samclip -v --max ?? work?

Sep 16 '19 00:09 tseemann

I want the soft-clipped fragments between 50 and 100 bp in the case. I did not realize the option -v, but that command should work for me.

Thanks Edison

Sep 16 '19 00:09 Edison2021

So you want the SAM lines where either end has been soft clipped between 50-100 bp?

Sep 16 '19 04:09 tseemann

A bit messy. Sorry about that, Let me describe what i am thinking now.
I would like to extract the soft-clipped sequences at either end if these soft-clipped sequences are longer than a defined value.

Best Edsion

Sep 16 '19 05:09 Edison2021