Error with Flash about crispresso HOT 2 CLOSED

Hi Charles,
It seems that in your experimental design you have a large amplicon of 464 bp but you can sequence only the ends of it since you are using 150bp PE.

Unfortunately you cannot use CRISPResso in this scenario since you cannot sequence the entire unmodified amplicon.

For paired end reads that means that any pair of reads should partially overlap. This is enforced since if you sequence only the ends of an amplicon you don't know what will happen inside and this will make the quantifications of indels wrong.

That is why FLASH is throwing this error since it is impossible to find any overlap for paired reads in your case.

Hope this is helpful

from crispresso.

Thanks. Yeah actually my case turned out my collaborators just gave me an amplicon sequence that was too long

from crispresso.