Loading reprocess_deposited_data.md +6 −2 Original line number Diff line number Diff line Loading @@ -16,5 +16,9 @@ Run these lines to modify the header and convert the format to be compatable wit 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 Move the resulting fastq.gz files into a new directoy. Modify the Move the resulting fastq.gz files into a new directoy (/fakepath/fastqfoler/). 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.\ Update the project name in config.example.yaml. Loading
reprocess_deposited_data.md +6 −2 Original line number Diff line number Diff line Loading @@ -16,5 +16,9 @@ Run these lines to modify the header and convert the format to be compatable wit 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 Move the resulting fastq.gz files into a new directoy. Modify the Move the resulting fastq.gz files into a new directoy (/fakepath/fastqfoler/). 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.\ Update the project name in config.example.yaml.
