Project: Transcriptome Annotation of Equus caballus
_{^{User Manual
03-713: Bioinformatics Data Integration Practicum
Team-2: Taylor Ayers, Tao Luo, Lilin Huang, Sarah Oladejo}}

Prepare the directory

git clone https://github.com/luotao9728/annotation

This directory contains files:

• start_pipeline.sh
• build_index.sh
• pipeline.sh
• annotation.yml
• README.md

Prepare the environment

1. Make sure Anaconda3 is installed on your computer
2. Make sure in your current working environment has the following packages:

• sickle-trim   (Trim illumina short reads)
• LoRDEC   (Fix long reads by short reads)
• hisat2   (Short RNA-seq Alignment)
• minimap2   (Long RNA-seq Alignment)
• seqtk   (Convert FASTA and FASTQ format)
• SamTools   (Sort and Convert sam to bam)
• StringTie   (Annotation)

3. Alternatively, you could directly create a new working conda environment using the following command (make sure you have annotation.yml file in your working directory):

conda env create -n annotation --file annotation.yml

conda activate annotation

Instruction for the pipeline

Requirements for input files

1. Reference genome: fasta/fna
2. illumina RNA-seq (forward/reverse): fastq
3. PacBio RNA-seq: fastq
4. Reference annotation: gff
5. Keyword: name of this annotation The input files should be in the annotation directory

1. Make sure you have the environment (with all packages) ready.
2. Download the input files into the cloned directory.
3. Execute the command and follow the prompt:

bash start_pipeline.sh

4. Follow the instructions to enter the file names.
5. Be patient. The annotation process may take a long time. Have a great day! :)