This program needs a fastq file as an input and will output quality files, trimed fastq files, sam files, bam files, sorted bam files and read normalized tdfs.
to download you will run:
git clone https://github.com/maallen3/mapandvischainonfiji.git
To run:
cd mapandvischainonfiji/
#if you are on fiji #module load python/2.7.14/pandas
python create_scipts_to_map_on_fiji_argparse.py infile.fastq outdir genome email
For example:
python create_scipts_to_map_on_fiji_argparse.py /scratch/Users/allenma/171025_NB501447_0179_fastq/Allen_Dowell-371/MA_DMSO_Groseq_S7_R1_001.fastq /Users/allenma/proseq/ hg19 allenma@colorado.edu
The output will be the following directories in your outdir: bams, bedgraphs, cutadapt, e_and_o, qsubscripts, qual, sams sortedbams, tdfs.
By default this script will create 5 slurm scripts and submit them all to the queue. infilerootname._mom_run.slurm #this script runs all the other scripts infilerootname._trim.slurm #this script trims the fastq files of adapters infilerootname.map.slurm #this script maps with bowtie2 infilerootname._samtobam.slurm #this script changes sams into bam files infilerootname._bamtobedgraph.slurm #this script creates normalized tdf files
For more options type python create_scipts_to_map_on_fiji_argparse.py --help
You can turn off the auto submit like this. python create_scipts_to_map_on_fiji_argparse.py infile outdir genome email --Turnoff_submit
If you turn on --flipreads one other script will be created and run.