Neurons specialized in encoding sound emerge before birth NatureComms
The samples were analyzed by first demultiplexing the fastq files using deindexer using the nextera index adapters and the 384 well layout. Individual fastq files were then mapped to mm10_ERCC genome using the STAR aligner using 2-pass alignment. Reads where filtered for only uniquely mapped and were saved in BAM file format, count matrices were subsequently produced. Estimated count matrices from all plates were combined into one data object, QC metrics were computed using scanpy function.
Second, from the same multiscale diffusion space, a KNN graph was generated . Force atlas was then generated from the neighbors graph using the tSNE coordinates as initialization . Finally, for a selection of leiden clusters, cells being far away from their members on the FA embedding were considered doublets. To detect them, pairwise distances were calculated and standardized, cells hazing ascore distance of more than 3 were considered doublets.
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