This repository contains the analyses scripts for the E2A/p53 infection manuscript:
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A1-A2: Illumina HiSeq4000 data were analyzed using Kallisto and Sleuth.
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B1-B2: Oxford Nanopore PromethION data were basecalled with Guppy in a Docker/enroot container. The samples were demultiplexed using pytrim2 on a Docker/Charliecloud container. The folders B1 and B2 contain the relevant scripts and Docker files. The containers were run on the LRZ Linux cluster cloud
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Demultiplexed ONT full-length reads were analyzed for differential gene expression using Oxford Nanopore's DEG transcriptome pipeline.
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C1: Gene expression data from Illumina and PromethION were integrated and analyzed.
The Illumina and PromethION data were submitted to GEO.