/RNAseQTL

Collection of scripts to map eQTL with RNAseq Data and Genotype by Sequencing

Primary LanguageR

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).