README.md

Amniote Gene Expression

Code used to explore the association of transposable elements (TEs) with gene expression during the Amniote evolution

Recommended programs

• CARP (https://github.com/carp-te/carp-documentation)
• SRA-Toolkit (https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/)
• RSEM (https://deweylab.github.io/RSEM/)
• BEDTools (http://bedtools.readthedocs.io/en/latest/)

Optional

• fastqc (https://www.bioinformatics.babraham.ac.uk/projects/download.html)
• Trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
• Bowtie2 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/)

Data used

• Genome (Downloaded from NCBI)
• RNA-seq (Downloaded from NCBI, Gene Expression Omnibus accession numbers GSE30352 and GSE97367, BioProject number PRJEB5206)
• Ortholog (https://asia.ensembl.org/info/website/archives/index.html)

Prerequisites

• Some level of familiarity with queuing systems (SLURM)

Workflow

1) Separate TEs into recent insertions or non-recent insertsion

1a) Download or acquire genomes of interest

6 genomes were downloaded from public databases (NCBI); All genomes were downloaded using wget, as recommended by NCBI (https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/). See Supplementary Table 1 for the source and assembly version of each genome used.

1b) Use CARP to identify and annotate TEs in the genomes

Details can be seen in https://github.com/carp-te/carp-documentation

1c) Separate TEs into specific classes

Code can be found in TESeparation

TO BE CONTINUED......