Closed edoardobertolini closed 1 year ago
@edoardobertolini Thanks for reporting this, and sharing your reproducible code, much appreciated! Investigating the problem right now and we'll get back to you soon.
@edoardobertolini The discrepancy comes from the fact that the addSpacerAlignments
and addSpacerAlignmentsIterative
has an argument standard_chr_only
set to TRUE
by default, which retains standard chromosomes for human and mouse, which is not relevant for other species; setting it to FALSE resolves this issue for your example.
The default should be set to FALSE
, we will change that immediately. Thanks!
Thank you!
Hi Jean-Philippe,
thanks for this great R package.
I would like to use crisprVerse package to design gRNAs in plant species and speed up the CRISPR construct design.
I have tested the package with the new sorghum genome (JGIv5) but I think something went wrong with the function addSpacerAlignmentsIterative
In particular, I do see differences in the results when I run the functions addSpacerAlignmentsIterative and runCrisprBowtie .
Although the parameter I used were the same ( bowtie, # mismatches, the two functions reported different results for the 21 spacers found :
Please see output below.
In addition, only few alignments derived from addSpacerAlignmentsIterative were properly stored in the S4 object guideSet:
For reproducibility, I have created a google drive folder with the data used and the R code to run the analysis: https://drive.google.com/drive/folders/1SP7ijDdpKqB1ElWSpfAyewIsM0CJm2lJ?usp=share_link
These are the outputs for a quick look:
[runCrisprBowtie] Using BSgenome.Sbicolor.JGI.sorBic5 [runCrisprBowtie] Searching for SpCas9 protospacers reads processed: 21 reads with at least one alignment: 21 (100.00%) reads that failed to align: 0 (0.00%) Reported 21 alignments [runCrisprBowtie] Using BSgenome.Sbicolor.JGI.sorBic5
[runCrisprBowtie] Searching for SpCas9 protospacers reads processed: 21 reads with at least one alignment: 21 (100.00%) reads that failed to align: 0 (0.00%) Reported 22 alignments [runCrisprBowtie] Using BSgenome.Sbicolor.JGI.sorBic5
[runCrisprBowtie] Searching for SpCas9 protospacers reads processed: 21 reads with at least one alignment: 21 (100.00%) reads that failed to align: 0 (0.00%) Reported 75 alignments [runCrisprBowtie] Using BSgenome.Sbicolor.JGI.sorBic5
[runCrisprBowtie] Searching for SpCas9 protospacers reads processed: 21 reads with at least one alignment: 21 (100.00%) reads that failed to align: 0 (0.00%) Reported 1384 alignments
[runCrisprBowtie] Searching for SpCas9 protospacers reads processed: 84 reads with at least one alignment: 84 (100.00%) reads that failed to align: 0 (0.00%) Reported 178 alignments
Thanks, Edo