Is it possible to analyze by inserting one mismatch guide RNA barcode?

[SujinKim13]

Hi,

CB2 program is very useful for analyzing pooled crispr screen.

I have one question. When I analyze the raw data, 1-2 mismatches are found in my fastq file.
So, Can I consider the 1bp mismatch via CB2?

Thanks,

Best regard,
Sujin Kim

[hyunhwan-jeong]

Hi @SujinKim13, CB2 doesn't support any mismatch alignment - my previous observation of the portion of the guide RNA with mismatch was marginal. Do you have any substantial amount of guides with mismatch?

Hyun-Hwan Jeong

[SujinKim13]

Hi @hyunhwan-jeong , Thanks for your reply. Depending on the case, about 20% of mismatches are found.

Sujin Kim

[hyunhwan-jeong]

Sorry for the late reply,

Do you mind sharing your data with [email protected]? Plus, I wonder how you could determine there were mismatches, did you use another alignment tool?