People involved (unordered) Elisa Dell'Aglio Agnès Vallier Mariana G. Ferrarini Théo Chancy Caroline Blanc Cristina Vieira Claire Hoede Christine Gaspin Rita Rebollo

Dataset Two RNAseq libraries from Marie Fablet. FastQC & Trimming Paired-end 100bp Sample Name M Seqs Trimmed

This tutorial was done by Rita Rebollo, Aurélie Huynh and Mariana Galvão Ferrarini, inspired by previous trials of Sho Miyake, Corentin Dechaud and Magali Naville. Nicolas Parisot helped with the fetch script. Install squire For us, squire does not work with star=2.5.3, so we installed it in conda with star=2.7.3a #new environment for squire with star 2.7.3.a conda create --name squire --override-channels -c iuc -c bioconda -c conda-forge -c defaults -c r python=2.7.13 bioconductor-deseq2=1.16.1 r-base=3.4.1 r-pheatmap bioconductor-vsn bioconductor-biocparallel=1.12.0 r-ggrepel star=2.7.3a bedtools=2.25.0 samtools=1.1 stringtie=1.3.3 igvtools=2.3.93 ucsc-genepredtobed ucsc-gtftogenepred ucsc-genepredtogtf ucsc-bedgraphtobigwig r-hexbin #activate environment source activate squire