Update reprocess_deposited_data.md

cat SRR19912835_1.fastq | awk '{if(NR%4==1) print "@"$2; else if(NR%4==2) print; else if(NR%4==3) print "+"; else if(NR%4==3) print $0}' | bgzip > speciesmix.ATAC.R1.fastq.gz\

cat SRR19912835_2.fastq | awk '{if(NR%4==1) print "@"$2; else if(NR%4==2) print; else if(NR%4==3) print "+"; else if(NR%4==3) print $0}' | bgzip > speciesmix.ATAC.R2.fastq.gz

3. Move the resulting fastq.gz files into a new directoy (/fakepath/fastqfoler/). \

3. Move the resulting fastq.gz files into a new directoy (/fakepath/fastqfoler/).

4. Update the rawdir and Project in Share_seqV2_example.sh accordingly:\

rawdir=/fakepath/fastqfoler/ \

Project=(speciesmix.ATAC) \

Start=Demultiplexed # this optine makes the pipepline awares the starting file is the demultiplex fastqs.\

Start=Demultiplexed # this optine makes the pipepline awares the starting file is the demultiplex fastqs.

5. Update the project name in config.example.yaml. 

6. Run the Share_seqV2_example.sh