This repo has code related to processing and quantifying the multiplexed DGE-seq data related to the CRISPRi and kinase inhibitor treatments. The processing pipeline involves a few simple scripts that take the sequencing results and split them into the sequencing reads from each well (see split_FASTQ_file.pl). Then takes each of the split sets of reads and gathers transcript read counts using salmon (see run_salmon_over_split.pl). Both of these scripts are a little bit rough, but have worked through this first pass at the data.
As for analyzing the results, I've put together three reports:
- DESeq2 Based Analysis - Using the R package DESeq2, I've compared the reads from each of the CRISPRi targets to the non-target wells.
- Transcriptome Correlation - This report covers calculating the correlation between the transcriptome in each of the wells.
- Bulk RNAseq Analysis - There is also some previously collected data related to the drug treatments tried in the DGE-seq, so I've reprocessed that sequencing data to produce the same type of report.