Additional file 3: of ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference

Figure S2. Trimming reads improves alignment of the GM12878 ATAC-seq reads. Tn5 transposase attaches mosaic end (ME) tags that need to be trimmed from the 5′ end of the read. Additionally, however, trimming low-quality base pairs from the 3′ end of the ATAC-seq reads so that all reads had the same length improved alignment to the genome (shown in green). With a 3 billion base pair genome, the chance that a sequence of a certain length will align randomly is high for sequences shorter than 17 base pairs. To minimize random alignment while removing low-quality base pairs for this ATAC-seq data, we trimmed the reads to a final length of 20 base pairs. (PDF 13 kb