Computational protocol: Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia

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Protocol publication

[…] Cell line authenticity and mutational analysis was performed as previously described []. Briefly, the raw RNA-seq data was aligned using the 2-pass method of the STAR (v2.5.1b) aligner [], followed by de-duplication, re-calibration and variant calling with the Genome Analysis Toolkit (GATK) Best Practices workflow (v3.5.0) []. The resulting variant calls were annotated using SnpEff and SnpSift (v4.2) followed by filtering and analysis using in-house Python and R scripts [, ]. […]

Pipeline specifications

Software tools STAR, GATK, SnpEff, SnpSift
Application RNA-seq analysis
Diseases Neoplasms
Chemicals Oxygen