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Analysis scripts for BFG-Y2H data

Project description

BFG Y2H Analysis Pipeline

Requirements

  • Python 3.7
  • Bowtie 2 and Bowtie2 build

Files required

The pipeline requires reference files and summary files before running. They can be found on GALEN:

all summary files contain summary of barcode information in csv format for yeast, human and virus
path: /home/rothlab/rli/02_dev/08_bfg_y2h/bfg_data/summary/
all reference files contain all the barcodes in fasta format
path: /home/rothlab/rli/02_dev/08_bfg_y2h/bfg_data/reference/

Before running the pipeline, you need to copy everything in these two folders to your designated directory.

An example sequence in output fasta file:

>G1;YDL169C_BC-1;7;up
CCCTTAGAACCGAGAGTGTGGGTTAAATGGGTGAATTCAGGGATTCACTCCGTTCGTCACTCAATAA

Running the pipeline

  • Install from pypi (recommend): python -m pip install BFG-Y2H==0.0.1

  • Install and build from github

1. download the package from github
2. inside the root folder, run ./update.sh
  1. Input arguments:
usage: bfg [-h] [--fastq FASTQ] [--output OUTPUT] --mode MODE [--alignment]
           [--cutOff CUTOFF]

BFG-Y2H

optional arguments:
  -h, --help       show this help message and exit
  --fastq FASTQ    Path to all fastq files you want to analyze
  --output OUTPUT  Output path for sam files
  --mode MODE      pick yeast or human or virus or hedgy
  --alignment      turn on alignment
  --summary      path to summary files (default is set to /home/rothlab/rli/02_dev/08_bfg_y2h/bfg_data/summary/)
  --ref      path to reference files (default is set to /home/rothlab/rli/02_dev/08_bfg_y2h/bfg_data/reference/)
  --cutOff CUTOFF  assign cut off (default is set to 20)
  1. All the input fastq files should have names following the format: y|hADDBGFP(pre|med|high) (for human and yeast)

  2. Run the pipeline on GALEN

# this will run the pipeline using slurm         
# all the fastq files in the given folder will be processed
# run with alignment 
bfg --fastq /path/to/fastq_files/ --output /path/to/output_dir/ --mode yeast/human/virus/hedgy --alignment

# if alignment was finished, you want to only do read counts
bfg --fastq /path/to/fastq_files/ --output /path/to/output_dir/ --mode yeast/human/virus/hedgy

Output files

  • After running the pipeline, one folder will be generated for each group pair (yADDB)

  • The folder called GALEN_jobs saves all the bash scripts submited to GALEN

  • In the output folder for each group pair, we aligned R1 and R2 separately to the reference sequences for GFP_pre, GFP_med and GFP_high.

  • *_sorted.sam: Raw sam files generated from bowtie2

  • *_noh.csv: shrinked sam files, used for scoring

  • *_counts.csv: barcode counts for uptags, dntags, and combined (up+dn)

Project details


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