Manchester Breast Center RNA-seq Protocol

Data process by aligment of Fastq files to GRCh38.p12   using STAR v2.5.1b and quantified at the gene-level with Gencode.v22 . Mismatching and multi-mapping reads and were excluded during alignment using the parameters "outFilterMisMatchNmax = 0" and "outFilterMultimapNmax = 1". Raw counts were normalised using the median ratio method implemented in the DESeq2 package (PDF ).

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