Computational protocol: A mouse model of hereditary hemorrhagic telangiectasia generated by transmammary-delivered immunoblocking of BMP9 and BMP10

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Protocol publication

[…] Reads were uploaded to the GobyWeb system and aligned to the 1000 genome human reference sequence with the STAR aligner. Ensembl annotations for transcripts were obtained from Biomart and Ensembl automatically using GobyWeb. Annotations were used to determine read counts using the Goby alignment-to-annotation-counts mode, integrated in GobyWeb in the differential expression analysis with EdgeR plugin. Counts were downloaded from GobyWeb as a tab delimited file and analyzed with MetaR. Statistical analyses were conducted with Limma Voom, as integrated in MetaR 1.7.2, using the rocker-metar docker image version 1.6.0.1. P-values were adjusted for multiple testing using the False Discovery Rate (FDR) method. Heat maps were constructed with MetaR, using the pheatmap R package. Gene annotations were determined with Ensembl/Biomart, using the biomart micro-language in MetaR. MetaR analysis scripts are presented in (). […]

Pipeline specifications

Software tools GobyWeb, STAR, edgeR, limma, voom, PHeatmaps
Applications RNA-seq analysis, Transcriptome data visualization
Organisms Mus musculus