Pipeline for mapping reads with bowtie (no mismtaches) to reference index (oligos included in the library) and UMI collapsing: oligo_UMISTARRseq_pipeline.sh
R markdowns for processing mapped reads, check quality of screens, replicates, and calculate activity of each oligo with DESeq2:
- Drosophila library: Drosophila_oligo_library_processing.Rmd
- Human library: Human_oligo_library_processing.Rmd
The raw sequencing and processed data are available from GEO under accession number GSE183939.
If you have any questions/requests/comments please contact me at bernardo.almeida94@gmail.com.