Resources

MPRA Protocol

If you want to follow our MPRA Protocol you can find a pdf document describing it here

MPRA Processing Pipelines

MPRAmatch and MPRAcount cover the first two steps of processing MPRA data. MPRAmatch aligns sequenced oligos with the reference and pulls the barcods associated with each sequence. MPRAcount takes the sequenced barcodes for each cell type tested and arranges a barcode level count table to be used for further analysis.

Both MPRAmatch and MPRAcount can be found here.

MPRAmodel performs an analysis of a barcode level count table and uses DESeq to determine activity and allelic skew of variants if present in the dataset.

MPRAmodel can be found here.

COVID-19 analyses

The Tewhey lab is working with the State of Maine to sequence positive COVID-19 samples from across the state and place them into a state-wide tree. The analysis pipeline being used can be found here, and the state-wide tree (including samples sequenced in other states of Maine residents) can be found here