min clip length

[Edison2021]

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

[tseemann]

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

[Edison2021]

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

[tseemann]

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?

[Edison2021]

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

[tseemann]

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

[Edison2021]

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