Genome-wide L1 insertion profiling of single neurons
L1 insertion profiling (L1-IP) amplifies genomic DNA flanking L1Hs insertions. L1-IP primers target nucleotides diagnostic of L1Hs. Sequencing reads (100bp single-end) are processed to remove from the 5' end: 1) an initial 5bp random nucleotides (used for cluster calling by the sequencer); 2) 5 or 6bp barcode; 3) an additional 5bp of random nucleotides incorporated by the L1-IP primers that prevent the barcode from biasing library PCR. 4) The 5bp seed of the primer, which can have mismatches relative to the reference. Reads were further processed to remove between 10 to 17 low-quality bases from the 3' end, depending on average quality scores of the sequencing run at each position.