crisprseq
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nf-core
A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the...
Description: I am running a CRISPR screening workflow using Bowtie2 for alignment and MAGeCK for counting. My input is an sgRNA FASTQ file, and my reference was initially in CSV...
### Description of feature For base editing/prime editing experiments, It would be nice to view the most common alleles and their frequencies. Would it be possible to include a table...
### Description of the bug Using the any design matrix with more then 3 samples there pipeline exists from Magick MLE with the following error. Command error: INFO @ Wed,...
bowtie alignment with latest nf version gives a different count matrix 🤯 _Originally posted by @matbonfanti in https://github.com/nf-core/crisprseq/issues/263#issuecomment-3557371687_
When running a MLE analysis from a precomputed count matrix and a contrast file, the pipeline does not work because in the changes of #252 the condition labels in the...
Hello, Thank you for such a great pipeline; it's been really helpful for our analysis. We've run a few hundred samples through different versions of the pipeline. When we reviewed...
### Description of feature Hi, I noticed there is a link to the usage guidelines page for how to create the samplesheet csv but upon following the link there is...
