PFB 2019 Final Project

Group members:

• Matthew Waas (TA)

• Doug Barrows

• John Werner

• Hunter Underhill

• Mina Kojima

• Becky Hennessey

• Zach Konkel

Our project is centered around providing users with a set of possible guide RNA locations for CRISPRa or CRISPRi given a set of gene IDs.

The approach is split into three parts

1. linking genes and start sites
2. creating a set of possible guides for a given PAM sequence
3. cross-refencing the list of start sites with the list of possible guides

More information on some functions:

FUNCTION: gff3_to_TSSbed

• Usage: gff3_to_TSSbed(gff3filename, outputfolder=".")

• INPUT: Takes a gff3 annotation file

• OUTPUT: bed file with the TSS site for all of the genes

FUNCTION: TSSs_of_interest_bed

• Usage: TSSs_of_interest_bed(TSSbedfile, genelistfile.txt, outputfolder=".")

• INPUT: 1) bed file with all TSSs, 2) gene name (or genelist in .txt format)

• OUTPUT: bed file with only the TSSs of interest

• Note about gene names:

  • can take either genenames (such as 'DMRT1') and Ensembl ID names (ENSGxxxxxxxxxx)
  • if a user-provided gene does not match a known genename or gene ID in the annotation file, provides user with a helpful message about the genes without a match

FUNCTION: convert_catpiss_output_to_gff3

• Usage: convert_catpiss_output_to_gff3(catpiss_output, scoretype, outputfolder='.')

• INPUT: output file from the catpiss program, with all gRNAs

  • also specify the "scoretype" to display in JBrowse

• OUTPUT: gff3 file to use for JBrowse

Visualization of designed sgRNAs in JBrowse

• Go to JBrowse site: crispr.programmingforbiology.org/jbrowse
• gRNAs colored by score:
  • Blue: score >50
  • Red: score <50