All the bioinformatics processing and analysis for plasma and saliva cfDNA used in W Lab. Created by Irene Choi.

NOTE: You only need to do this once. Hoffman2 has most dependencies already preinstalled. Follow the steps below to install all the ones Hoffman2 does not already have.

bbmap

1. Click on this link: https://sourceforge.net/projects/bbmap/.
2. Download bbmap and unzip.
3. Drag and drop unzipped bbmap folder into Hoffman2 home directory.
4. Double check that you have bbmerge.sh within the bbmap folder in Hoffman2 home directory.

fastp

1. Click on this link: https://github.com/OpenGene/fastp.
2. Go to this section: or download the latest prebuilt binary for Linux users.
3. Download by running this command on Hoffman2.

wget http://opengene.org/fastp/fastp
chmod a+x ./fastp

4. Double check that you have fastp in Hoffman2 home directory.

qualimap

1. Click on this link: http://qualimap.conesalab.org/.
2. Go to this section: Downloads.
3. Download qualimap_v2.2.1.zip and unzip.
4. Drag and drop unzipped qualimap_v2.2.1 folder into Hoffman2 home directory.
5. Double check that you have qualimap_v2.2.1 in Hoffman2 home directory.

srsly-umi

1. Click on this link: https://www.claretbio.com/products/srsly-umi.
2. Go to this section: Option 1.
3. Load Python on Hoffman2.

module load python

4. Download by running this command on Hoffman2.

pip install srslyumi

umi_tools

1. Click on this link: https://umi-tools.readthedocs.io/en/latest/QUICK_START.html.
2. Go to this section: Step 1: Install UMI-Tools.
3. Load Python on Hoffman2.

module load python

4. Download by running this command on Hoffman2.

pip install umi_tools

picard

1. Download picard.jar from this GitHub.
2. Drag and drop picard.jar into Hoffman2 home directory.

NOTE: This is a sketchy way of downloading it. This will have to do for now. Make sure it looks like a coffee mug!

blacklist regions

1. Download blacklist.bed from this GitHub.
2. Drag and drop blacklist.bed into Hoffman2 home directory.

NOTE: These are the blacklisted regions we are removing!

NOTE: Please make sure all the packages are downloaded before running the scripts!

Scripts use 3 arguments:

1. Directory of your input file (DO NOT INCLUDE FILENAME!)

/u/INPUT_DIRECTORY/

2. Name of the sample file (DO NOT INCLUDE DIRECTORY!)

NOTE: You should have a pair of files. Please change the name to SAMPLE_R1.fastq.gz and SAMPLE_R3.fastq.gz if not already done so!

FILENAME

3. Directory of your output file (DO NOT INCLUDE FILENAME!)

/u/OUTPUT_DIRECTORY/

For example, you can run the following command to submit as a job on Hoffman2:

qsub run_pipeline_saliva.sh /u/home/c/choi/ S_H7 /u/scratch/c/choi/saliva/

This means I have the pair /u/home/c/choi/S_H7_R1.fastq.gz and /u/home/c/choi/S_H7_R3.fastq.gz of files that I want to process! I want to output my processed files into the directory /u/scratch/c/choi/saliva/.

NOTE: Please make sure all the samples have been pre-processed before running the scripts! Each script requires a different set of arguments. Please check each individual analysis script before!

peaks_n_valleys.py

1. Download peakdetect from this repo: https://github.com/avhn/peakdetect/.
2. Run peaks_n_valleys.py after changing/renaming the input for samples within the python script.