RNAseQTL

Collection of scripts to map eQTL with RNAseq Data and Annotated Variants. To map eQTL we need two files:

1. Gene expression counts matrix;
2. Genotype of the animal model (0 homozygot reference, 1 hereozygote alternative, 2 homozygote alternative);

Summary

RNAseQTL is a collection of scripts to map cis-eQTL. The pipeline is designed getting transcriptomic from RNA-seq data and variants annotation in VCF file format.

Requirements

RNAseQTL requieres the following softwares:

• FastQC

• Tophat2/Bowtie2

• HTSeq-count

• VCFtools

• plink 1.9

• R

• BioMart

• GenomicFeatures

• Matrix-eQTL

The pre-built indexes of the reference genome could be downloaded in ENSEMBL or in the iGenomes website (http://support.illumina.com/sequencing/sequencing_software/igenome.html).