Hello, stranger

this is a pipeline for running through all of the software necessary for genomic alignment

• install.sh -- installs all necessary software and packages on a fresh computer or server
• pipeline.sh -- wrapper for align.sh that puts everything in a tmux session
• align.sh -- script that runs through the list of alignment software below

1. FastQC
2. cutadapt
3. FastQC (again)
4. Tophat
5. Cuffquant

1. ssh into the server that you want to run the alignment on.
2. run the install.sh script if you don't have all the software you need yet.
3. if needed, git clone this repository somewhere on the server.
4. download and create all the .gff, .bt2, .ver, and .fa reference files that you need for the Dog genome and place them into the dog directory, same for mouse directory. Label them latest_dog_genes/latest_mouse_genes.
5. run chmod +x *.sh in this repo to make everything executable.

You are now ready to run the pipeline! First cp or mv the .fastq files you want into the same directory as the scripts.

./pipeline.sh start

• answer all the questions that it asks you, such as how many cores you want to use, the species you are aligning to, etc. Press ENTER through all the prompts to start the pipeline.
• the script makes a new tmux session and starts the align.sh script under it. If there is already a session open, it will run it under that session (I think).
• you can close out of the ssh session or terminal window that you are running from and the script will continue to run.

./pipeline.sh attach

• when you want to check on the progress of the pipeline, run this
• this will connect the tmux session to your current terminal or ssh window and show you the current output of the running pipeline

tmux detach

• you can run this inside the tmux window to get back out into your terminal or you can close the window but this is probably safer

the .gitignore file should ignore all the genomic files like

1. *.bt2
2. *.fa
3. *.fa.fai
4. *.fa.tlst*.fastq
5. *.fastq.qz
6. *.gff
7. *.ver

but if you see any git pushes taking an abnormally long amount of tmie, Ctrl+C that shit so we don't crash github.