Bash and R scripts to analyze Next-Gen sequence data.
Contact: Eric Garcia, e1garcia@odu.edu
Simple script to create sequence quality reports (FASTQC and MultiQC) in parallel with a single command on a remote HPC
Usage - Place script in same directory as files to be processed and execute specifying the extension of files between quotations. For example:
sbatch Multi_FASTQC.sh "fq.gz"
Multi_FASTQC.sh has been tested in "fq", "fq.gz" and "bam" files.
Open script for more details
This script counts the number of each base in DNA fragments from single-digest Sbf1 RADseq, pair-end fq.gz files according to the window size and region determined by user
Usage:
1.- Place script in the same directory with files to be processed. Open script and:
2.- Set slurm options according to your system
3.- Set "User Variables"
4.- Check that the ls statement in line 69 will list your input files. Modify regex if necessary
5.- Execute in command with: sbatch <script name> <"readDir">
sbatch base_calculator.sh "F"
Output:
- TSV table with file names, base counts, and read information.
Open script for more details
R script to calculate, and plot, base pair proportions and mean base pair proportion of DNA fragments position by position
Uses the output of base_calculator.sh, or tsv files with base pair counts from single digest RADseq, paired-End sequencing data, as input
Open script for more details
read_caltulator.sh counts the number of reads in compressed (default) or uncompressed FQ files (open script for details).
Usage:
1.- Place script in the same directory with FQ files to be processed. Open script and:
2.- Set slurm options according to your system
3.- Set "User Variables"
4.- Execute
sbatch read_calculator.sh
Output:
- CSV table with file names and total number of reads
motif_calculator.sh identifies and counts repeated motifs in compressed or uncompressed FQ files
Usage:
1.- Place script in the same directory with files to be processed. Open script and:
2.- Set file and read info as well as the maximum length (bp) of motifs to be counted.
motif_calculator.sh will then lists and reports frequencies of all motifs within the size range of "position 1", or the first bp, to the specified maximum length (from beginning of reads only).
User variables options:
FILE_DIRECTION ("forward" or "reverse")
DIRECTION_SUFFIX ("F","R","R1","R2", etc)
FILE_EXTENSION ("fq" or "fq.gz" for uncompressed and compressed files, respectively)
MAX_motif_length (digit)(maximum motif size (in bp) to search for repeats)
THREADS (number of threads according to your system)
Open script for details
fq_repeat_cleaner.sh removes sequences with repeated motifs at the beginning of the read in compressed or uncompressed FQ files
Usage:
1.- Place script in the same directory with files to be processed. Open script and:
2.- Set file and read info, maximum length (bp) of motifs to be counted, and output base name.
3.- Execute and once the motif frequencies are printed in the terminal, enter the the desired motif length to base the read removal.
Output:
One single concatenated FQ file (from all input files) with all reads for which the starting motif of predetermined length does not repeat in any other reads
Open script for details
Simple script to concatenate files of the same individuals but from multiple sequencing lanes
Usage: Open the script can enter your files' read and lane info
User friendly list of steps and code to successfully subset VCF files while maintaining functionality
Use this code to maintain a stable ssh connection if your sessions are becoming idle and/or terminated very quickly, after 1-2 min of inactivity.
Instructions on how to run mapDamage on Wahab ODU's cluster. See file for details