Question: CRISPResso analysis software
gravatar for ramonaramonawan
4.0 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 • 1.5k views
ADD COMMENTlink written 4.0 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 4.0 years ago by genomax91k

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 4.0 years ago by ramonaramonawan10
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