Hi, a stupid question, is crispr-seq pipeline based out of mageck?

It contains certain mageck functions yes

I assume, the counts, mle and rra all are included? I am trying to map the sgrna seq libray to fastqs and tried mageck as well as nf-core, both are skipping the negative control. Not sure why?

Could you give me your command line?

1. nextflow run nf-core/crisprseq -r dev --input samplesheet_w_control.csv --mle_design_matrix design_matrix.txt --library final_input_sgrna.tsv --contrasts contrast_file.csv --analysis screening --outdir /home/ap764/mageck/output -profile conda

2. nextflow run nf-core/crisprseq -r dev  --input samplesheet_w_control.csv --mle_design_matrix design_matrix.txt --rra_contrasts contrast_file.csv --library final_input_sgrna.tsv --analysis screening --outdir /home/ap764/mageck/output_final_rra -profile conda

I will send you a way to add the negative controls because right now they're not specified right?

It is present in my

samplesheet_w_control.csv