Comparison of input DNA profiles obtained by microarray and sequencing technologies. (a) A genome browser view of input DNA profiles of chromosome 2R of D. melanogaster at various developmental stages measured by microarray (INPUT-chip; blue) and sequencing (INPUT-seq; red). (b) A heat map that summarizes the Spearman correlation coefficient between every pair of the nine INPUT-seq and eight INPUT-chip profiles along with genome-wide GC content. The number of mappable reads (in million) is written next to the name of each INPUT-seq profile. (c) The average signal profiles of INPUT-seq and INPUT-chip around transcription start sites (TSSs) and transcription end sites (TESs) are largely consistent, and their variation along these genomic regions generally coincide with GC content variation. (d) We generated 11 additional profiles from one of the INPUT-seq samples (AM) by subsampling the reads at different proportions (90%,80%,...,10%,5%,1%). A heat map summary representation of the Spearman correlation coefficient between every pair of sub-sampled INPUT-seq profiles and GC content is shown here. (e) The relationship between sequencing depth and genomic coverage. The curve shows how sequence read subsampling (i.e., reducing sequencing depth) affects genomic coverage. The genomic coverage of the nine INPUT-seq datasets and our Agilent microarray are also shown in the plot.
Ho et al. BMC Genomics 2011 12:134 doi:10.1186/1471-2164-12-134