## Written by Nader Atlasy ##
### The mapping aligner code and parameters used to map the Read1 sequencing data against a hybrid genome assembly of hg38+mm10 ###

STAR --runThreadN  40 --runMode alignReads --outFilterMismatchNmax 1 --outFilterMultimapNmax 1 --outSAMtype SAM --genomeDir /home/natlasy/genome_indeces/hybrid_hg38_mm10_ERCC_RP/ --readFilesIn ./"$sampleSEQ"."$samplName".1.fastq --outFileNamePrefix ./"$sampleSEQ"."$samplName".hybrid. --sjdbFileChrStartEnd /home/natlasy/star/genome_indeces/hybrid_hg38_mm10_ERCC_RP/sjdbList.fromGTF.out.tab --sjdbOverhang 42



### Counting the reads against hybrid reference genome of hg38+mm10 ### 
htseq-count -m union -s no -t exon -i gene_id InPut /home/natlasy/star/genome_indeces/hybrid_hg38_mm10_ERCC_RP/all.gtf > SaMple.hybrid.counted