No matches using count_spacers

[Mehmet Hazirci]

Hi All, 

I am using the GeCKO v2 library, and have followed the protocol from Joung et al. Nature 2017 in regards to amplifying the library aswell as performing the necessary PCR reactions. 

These are the results from using count_spacers function on my fastq file. I can send my code if anyone wants to have a look at it. I greatly appreciate any help with this as I'm completely stuck. All counts in the library_count csv are 0. 

7

[Julia Joung]

Hi Mehmet,

Thank you for your interest in our work.

Based on your output, it looks like the key regions were found in most of your sequences, but the identified guide sequences in your reads did not match your library. Most likely, you will need to add or remove the '-no-g' flag depending on whether guanine was added 5' to your guide target sequences.

Best,

Julia

--
You received this message because you are subscribed to the Google Groups "Genome Engineering using CRISPR/Cas Systems" group.
To unsubscribe from this group and stop receiving emails from it, send an email to crispr+un...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/crispr/904ddc0a-bc7d-4705-a192-65ccf26ff421n%40googlegroups.com.