search

lucapinello / CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
Other
131 stars 55 forks source link

mutation frequency plot #30

Closed frankbioinfo closed 6 years ago

frankbioinfo commented 6 years ago

hello @lucapinello

Thank you for your help so far, i was able to get CRISPResso working, I had a question with respeect to the mutation frequency plot, as seen below

screen shot 2017-11-01 at 3 19 36 pm

What could be reason we seen peaks at the beginning and end of the sequence, I can see this in almost all my sequences i did used '--trim_sequence' for trimming adapters.

Thank you once again

lucapinello commented 6 years ago

Hey Frank,

This is very common for samples where you have trimming artifacts. The trimming operation may not be perfect with your sample. Since you are using the window strategy and those events are far away from the cleavage site you can safely ignore them (since they will not be quantified).