Update README.md

# Important note

The ATAC and RNA barcodes would in the format of R1.xxx,R2.xxx,R3.xxx,P1.yy, where xxx is in the range of 01-192, yy is in the range of 01-96.\

The P1.xx indicates the primers that were used to amplify each ATAC and RNA sub-libraries. It is expected to be different between RNA and ATAC assay. The rest part of barcode (R1.xx,R2.xx,R3.xx) would be the same for ATAC and RNA library.\

Depending on the downstream analysis pipeline, sometimes the comma in the barcode would be converted to period (R1.xx,R2.xx,R3.xx,P1.xx --> R1.xx.R2.xx.R3.xx.P1.xx).\

The P1.xx indicates the primers that were used to amplify each ATAC and RNA sub-libraries. It is expected to be different between RNA and ATAC assay. The rest part of barcode (R1.xxx,R2.xxx,R3.xxx) would be the same for ATAC and RNA library.\

Depending on the downstream analysis pipeline, sometimes the comma in the barcode would be converted to period (R1.xxx,R2.xxx,R3.xxx,P1.yy --> R1.xxx.R2.xxx.R3.xxx.P1.yy).\

A barcode translation table indicating the P1.xx used in the assay would be beneficial, when submitting data to GEO.

# Installation

This pipeline requires following packages to be properly installed and added to system path: GNU parallel, Bcl2fastq, fastp, zcat, STAR, bowtie2, python2, umi_tools, samtools, picard (2.14.1, newer version may result in error), R, featureCounts, read_distribution.py from RSeQC, bedtools

This pipeline requires following packages to be properly installed and added to system path: GNU parallel, Bcl2fastq, fastp, zcat, STAR, bowtie2, python3, umi_tools, samtools, picard (2.14.1, newer version may result in error), R, featureCounts, read_distribution.py from RSeQC, bedtools. 

The SHARE-seq-alignment scripts can be directly downloaded from the github website.\

[https://github.com/masai1116/SHARE-seq-alignment/](https://github.com/masai1116/SHARE-seq-alignment/)

After downloading all scripts, update the general configuration section in main script "Split_seq_example.sh":

1) myPATH # where the SHARE-seq scripts are installed. e.g. myPATH='/mnt/users/Script/share-seq-github-v1/'

2) pythohPATH # where python2 is installed e.g. pythohPATH='/usr/bin/python' 

2) pythohPATH # where python3 is installed e.g. pythohPATH='/usr/bin/python' 

3) picardPATH # where picard is installed e.g. picardPATH='/mnt/bin/picard/picard.jar'

The pipeline also requres gtf files and aligner index files to be download and unziped into the right location.\