P-GSE40810-4 - P-GSE40810-4

Type
feature_extraction
Description
The image analysis and base calling were performed with the Illumina package OLB (v1.8). We used SolexaQA(v1.9) to assess the quality of data and then used DynamicTrim.pl to cut off the low-quality part . Sequence reads were mapped onto the reference mouse genome (NCBI Build UCSC mm9) using Bowtie (v0.12.7) algorithm (Langmead et al. 2009). Extend 350bp from 5' end of read as end site of fragment due to our library fragment length was ~200-500bp, center at about 350 bp. Genome_build: mm9 Supplementary_files_format_and_content: [bed format] chrom: The name of the chromosome scaffold.chromStart: The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.chromEnd: The ending position of the feature in the chromosome or scaffold.name: Defines the name of the BED line. score: A score between 0 and 1000.strand - Defines the strand - either '+' or '-'.
Links
Experiment E-GEOD-40810