undergraduate_level_cfDNA_lab

Generate simulated "sam-like" files for teaching students how to handle cell-free genomic data

Intention

This lab was created to help students familiarize themselves with genomic data. The scripts here create "Sam-like" files that are tsv's with READID , CHR, START, END, TLEN, although any sam column can be added.

How to use

The script will take in a genome file and index it if needed. This genome file can be something like hg19, or hg19 concatenated with microbial genome if infection is something you want to study.

Diseases simulated

1- Aneuploidy in pregnant women 2- Transplant rejection 3- Bloodstream infection

The data generated has length and fragmentation patterns typically found in cfDNA experiments

Use

python scripts/generate_sam.py --num_reads 1000000 \
                              --genome_file PATH_TO_FASTA \
                              --length_distribution_file PATH_TO_FILE \
                              --patient_sex (M or F) \
                              --output_fle (outfile) \
                              --BSI_reads (number of reads for bloodstrem infection simulation) \
                              --donor_sex (M or F) \
                              --donor_frac (float) \
                              --chr_21_fraction (float) \