Question: CRISPResso analysis software
gravatar for ramonaramonawan
4.2 years ago by
ramonaramonawan10 wrote:

Hi, I got the sequencing data of Miseq, and tried to use CRISPResso to do the analysis since I am using CRISPR to cut the target gene. However, my sequencing molecules do not start with the same nucleotide since I also add some barcodes beyond my PCR primers with different length. I tried to trim the primer sequences off my products, so I could get the same start and same end for all my sequences. As I read from CRISPResso, we could use trimmomatic plus sequence we want to get ride of. However, it did not work for me, and no primer sequences were trimmed. I am wondering if anyone has any suggestions? or you have better ways to analyse the mutations or indels produced by CRISPR/Cas9? Thanks Ramona

btw: my command for trimmomatic in CRISRPesso was: --trimmomatic nnnnnnn (sequence to be trimmed)

sequencing • 1.7k views
ADD COMMENTlink written 4.2 years ago by ramonaramonawan10

Are the padded sequences fixed length? If so you could use trimmomatic (outside CRISPResso) to do a CROP and remove them.

ADD REPLYlink written 4.2 years ago by GenoMax94k

no, actually the padded sequences are not of fixed length, they range from 0 to 9 nucleotides, it is just for the sequencing sake.

ADD REPLYlink written 4.2 years ago by ramonaramonawan10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2241 users visited in the last hour