- design fetures better reflecting technology
- better training data
- better deep learning method
Simulate from chr1
to calculate number of reads (N) N=(cov * G)/rl
For chr17, cov=30, rl=200 2x100bp N=(30 * 83M)/ 200==8M reads to be simulated using this command
Using WGS
/u/scratch2/n/ngcrawfo/ERROR_CORRECTION/wgs_simulation/wgsim/wgsim -r 0.03 -R 0.005 -e 0.02 -1 100 -2 100 -A 0 -N 8000000 /u/home/s/serghei/project/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/17.fa WGS_chr17_1.fastq WGS_chr17_2.fastq >log
The output of this command (written to log file) has this format:
- Col1: chromosome
- Col2: position
- Col3: original base
- Col4: new base (IUPAC codes indicate heterozygous)
- Col5: which genomic copy/haplotype
Reads are simulated here /u/home/s/serghei/scratch/WGS_deepSNP
Now i am mapping using BWA
bwa mem ~/project/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/17.fa WGS_chr17_1.fastq WGS_chr17_2.fastq | samtools view -bS - > WGS_chr17.bam
qsub -cwd -V -N bwa -l h_data=16G,time=10:00:00 run_BWA.sh
/u/home/s/serghei/scratch/WGS_deepSNP
- Train on simulated apply on real?