Fig. 1
From: LAMPS: an analysis pipeline for sequence-specific ligation-mediated amplification reads
Schematic of the LAMPS analysis pipeline. LMA reads are mapped to the set of possible primer pairs (F-F, F-R, R-F, and R-R). If the sequenced library is multiplexed, the frequency count of each primer pair per barcode is obtained. Reads that are too short or could not be mapped initially (‘Unmappable’) are remapped to individual primer sequences. For 1D data, ‘On-diagonal’ read counts of expected primer pairs (gray entries of the F-R quadrant) are then normalized and outputted in bedGraph format. For 2D data, the entire F-R quadrant is provided as output in raw contact frequency matrix format