Citation: C. Ulpinnis (2017-02-07): RNA-Seq_Pipeline_MA.
Abstract: The published scripts are integrated in a pipeline which was developed at the IPK in the frame of a master thesis. The pipeline aims to perform a gene prediction in genomic data using additional information from RNA-seq data. The process is divided into four main steps that integrate several external tools: 1) RNA-Seq-Scaffolding (L_RNA_Scaffolder), 2) repeat masking (Kmasker), 3) RNA-seq alignment (STAR or HISAT2) and 4) gene prediction (GeMoMa). The pipeline is developed to work at the computing infrastructure of the IPK.
License: CC BY 4.0 (Creative Commons Attribution)
| modules | |
| braker_run.sh | 2.7 KB |
| gemoma_run.sh | 4.1 KB |
| general.conf | 161 B |
| modulefunction.sh | 3.5 KB |
| module_test.sh | 659 B |
| pipeline.sh | 7.8 KB |
| project.conf | 550 B |
| CONTRIBUTOR: | |
| CREATOR: |
Chris Ulpinnis
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| PUBLISHER: | Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Corrensstraße 3, 06466, Germany |
| SIZE: | 0 B |
| SUBJECT: | RNA scaffolding, gene prediction, scripts |