MERFISH pipeline

[lisa-sousa]

• revise primer generation
• revise readout probes generation
• revise codebook implementation
• check if pipeline has all required property filters
• check if pipeline has correct blast specificity parameters
• check if pipeline has correct blast corss-hybridization parameters
• add to pipeline the set scoring function + check if distance parameter has big influence on number of probes generated
• assemble final probe → Primer1(T):A:RP1:A:target:A:RP2:T7(rc)

[lisa-sousa]

Merfish pipeline created in refactor branch.
Missing points: check and adapt final specificity Blast for tRNA+rRNA / HEG

• add function that retrieves all rRNA / tRNA gene names that can be used to filter the reference database → add filter function to genomic region generation for “gene_biotype” which works for ensemble and ncbi
• read highly expressed genes user input and filter reference database for them