Make STAR index and other refs:

• (optional for DE analysis) concat deaminases sequence with GRCh38
• (optional for DE analysis) concat deaminases gtf annotation with gencode v40 basic gtf
• samtools faidx
• picard CreateSequenceDictionary
• make chromosome bed files (for run mpileup in parallel) ./chrBed, chromosome length from GRCh38

Run run_STAR.sh. I put each pair of paired-end fastq.gz files in a subfolder

for dir in ./*/
do
cd $dir
echo $PWD
qsub -cwd -pe smp 4 -l h_rt=336:00:00 -l mem_free=15G ../run_STAR.sh 
cd ..
done

• STAR alignment: need to trim 3' illumina universal adapter
• samtools sorting etc
• picard MarkDuplicate
• gatk SplitNCigarReads
• split by read orientation

run bcftools mpileup for variants calling. I split up files by chromosome and strand for parallel computing.

Custom R script (vcf_preprocess.R) to reformat vcf files, convert DNA alt to RNA alt, and basic filtering

• If refs have extra chromosomes, remove ##contig lines to only keep chr1-23, X, Y, M;

concat all [strand_chr].vcf files for downstream editing site calling. (so multiple test correction is done tx-wide)

Edit_call_cmh.R