P-GSE40548-3 - P-GSE40548-3

Reads were mapped to the human genome (hg19) using TopHat (v1.4.1). Illumina libraries:default TopHat parameters were used with the addition of the -g / --max-multi-hits option set as 1, to report only uniquely mapping reads. SOLiD libraries: preliminary analysis of read quality scores showed a decrease in quality of SOLiD reads towards the 3’ end of the read, and consequently reads were trimmed by 10 bases from the 3’ end and first mapped to the human genome using Bowtie (v0.12.7). Reads not uniquely mapped by Bowtie were then mapped using TopHat and the two datasets merged. Gene annotation and calculation of RPKM values was carried out using Cufflinks (v1.3.0) with the provision of a GTF annotation file (hg19). Genome_build: hg19 Supplementary_files_format_and_content: Files were created using cuffdiff applying a 5% false discovery rate and with the provision of a reference GTF (hg19)
Experiment E-GEOD-40548