P-GSE45517-4 - P-GSE45517-4

normalization data transformation protocol
All sequenced tags were trimmed and mapped to the mouse genome (mm9) by using Bowtie (version 0.12.2-0.12.7). Generally, two mismatches were allowed in the first 25nt region and only those tags with one unique hit in the mouse genome were kept. Multiple tags mapped to the same genomic position were collapsed into one or up to 4 tags to remove potential PCR amplicons. Density files were generated by using bedItemOverlapCount and wigToBigWig programs from UCSC kent source package. Different density files in group of experiments such as WT and KO were normalized to same number of total mapped reads for comparision. Genome_build: mm9
Experiment E-GEOD-45517