2011-10-27

Expression estimation and tests for differential expression were processed by Cufflinks program v0.8.3. Cufflinks uses the normalized RNA-Seq fragment counts to measure the relative abundances of transcripts. The unit of measurement is Fragments Per Kilobase of exon per Million fragments mapped (FPKM). Reference genome: hg19. For the detection of variants,aligned files from the three different aligners (see publication) were processed with SAMtools and subsequently with VarScan (v2.2) for Single Nucleotide Variations (SNVs) detection. Variance calling was constrained to locations within gene regions with at least 10X coverage, variation frequency of more than 30% and base quality of more than 15. By subtracting variation between tumor and the matched NT sample, somatic single nucleotide variations were obtained and compared to NCBI dbSNP Build 131. Lastly, we intersected the somatic SNVs detected from all three aligners to derive a set of high confidence SNVs

Lin, CH, Lok, S. (2011). GSM823521: HCC473T. [Data File]. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM823521

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