Currently, CERES assumes that sgRNAs have 20 nts before the PAM in the function guideAlignments. However, some libraries use 19 nt guides. Ideally this could be solved by taking the alignment end rather than the beginning for positive strand alignments. Simple hack that worked for me instead: add an argument guide_length to the guideAlignments call signature. guide_length can be determined in map_guide_to_locus by checking the number of characters in the first entry in guides (assumes all guides are the same length).
j-g-b
commented
6 years ago
Currently, CERES assumes that sgRNAs have 20 nts before the PAM in the function
guideAlignments. However, some libraries use 19 nt guides. Ideally this could be solved by taking the alignment end rather than the beginning for positive strand alignments. Simple hack that worked for me instead: add an argumentguide_lengthto theguideAlignmentscall signature.guide_lengthcan be determined inmap_guide_to_locusby checking the number of characters in the first entry inguides(assumes all guides are the same length).