- Pre-built reference file located on galen:
/home/rothlab/rli/02_dev/mgy_pipeline/ref/S288C_reference_sequence_R64-2-1_20150113
usage: main.py [-h] [--fastq FASTQ] [--output OUTPUT] [--ref REF]
[--ploidy PLOIDY]
MGY analysis
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
--ref REF path to all reference files
--ploidy PLOIDY Ploidity (default set to 1)
-
Run the alignment and variant call (submit jobs to slurm). Command example:
python main.py --fastq path/to/fastq --output path/to/output --ref path/to/ref -
Run the analysis script for individual vcf file (no jobs submitted, takes around 1-2hrs)
usage: compare.py [-h] [--p P] [--c C] [--f F]
Process some integers.
optional arguments:
-h, --help show this help message and exit
--c C CDS
--f F Input vcf file
Example
python compare.py --c path/to/cds.txt --f output/from/main