maximum guide length

[LdeDiaz]

I have had great success using CB2 for CRISPR studies and greatly appreciate your work on this package!

I have a project where I am looking to analyze enrichment of guide pairs, rather than individual guides. In another workflow, I simply merge the two guide sequences in my fasta reference files and also merge the two reads together from the fastq files, making a 42mer in each file that is quantified by a simple kmer match. I have so far been unsuccessful in using CB2 to quantify the guides when they are merged. I have have been able to confirm that the individual guides can be quantified properly by CB2 and that the kmer matching workflow I have used in the past is able to quantify the merged guides properly.

Can you please let me know what is the limit in guide length allowable to search with CB2?

Many thanks!

[hyunhwan-jeong]

Hi @LdeDiaz,

Thanks for reaching to us! The problem is caused due to CB2 only supports guides <= 30mer due to an algorithm limitation. I am interested in supporting the feature in CB2, it would be great if you can provide the following information:

• From my understanding, your data seems to be a paired-end FASTQ, and each end contains one guide with adapter sequence. Is it correct?
• How many guides/possible guide-pairs are included in your library?
• Wouldn't the statistical test be changed? Do you have any specific hypothesis test you want to try?
• If possible, could you provide some test data for guide library & FASTQ (for FASTQ you can provide the first few reads) to test the new implementation?

Best regards,

Hyun-Hwan Jeong

[hyunhwan-jeong]

@LdeDiaz, I wonder if you are still interested in supporting the function. If so, could you provide the details regarding my questions?

Thank you,

Hyun-Hwan Jeong