## STAR Aligner v2.5.3a
## Creating Genome Indices,  Fasta files were downloaded from UCSC Genome Data. Only Canonical Chromosomes were used including X, Y and M.

/Path/To/STAR --runMode genomeGenerate --runThreadN 10 --genomeDir /Path/To/Genome/Directory_to_be_creates/   --genomeFastaFiles /Path/To/Fasta/Files

##Mapping Script For ATAC-Seq Libraries:

/Path/To/STAR --runThreadN 10 --genomeDir /Path/To/Genome/Index/ --readFilesIn /Path/To/Library_R1.fq.gz /Path/To/Library_R2.fq.gz --readFilesCommand zcat --outFileNamePrefix /Path/To/Output/FileName --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 2 --outFilterMismatchNmax 3 --alignIntronMax 1 --alignEndsType EndToEnd



##Mapping Script For RNA-Seq Libraries:

/Path/To/STAR --runThreadN 10 --genomeDir /Path/To/Genome/Index/ --readFilesIn /Path/To/Library_R1.fq.gz /Path/To/Library_R2.fq.gz --readFilesCommand zcat --outFileNamePrefix /Path/To/Output/FileName --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterMultimapNmax 2 --outFilterMismatchNmax 3

