Loading reprocess_deposited_data.md +6 −1 Original line number Diff line number Diff line Loading @@ -4,10 +4,15 @@ The SHARE-seqV2 alignment pipeline generates a pair of fastqs for each sample. T We have deposited SHARE-seqV2 data on [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207308) As an example, we can download the species mixing ATAC SRA record by fasterq-dump -A SRR19912835 --split-files -p This will generate two fastq files: SRR19912835_1.fastq and SRR19912835_2.fastq The read header looks like:\ head -4 SRR19912835_1.fastq\ @SRR19912835.1 A01389:111:H2Y5KDMXY:1:1101:1127:1000_R1.003,R2.032,R3.081,P1.06 length=50\ GGGCTACACAGAGAAACCCTGTCTCGAAAAACAAACAAAACAAAACAAAA\ +SRR19912835.1 A01389:111:H2Y5KDMXY:1:1101:1127:1000_R1.003,R2.032,R3.081,P1.06 length=50\ FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:\ FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: Run these lines to modify the header and convert the format to be compatable with SHARE-seq pipeline. 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 Loading
reprocess_deposited_data.md +6 −1 Original line number Diff line number Diff line Loading @@ -4,10 +4,15 @@ The SHARE-seqV2 alignment pipeline generates a pair of fastqs for each sample. T We have deposited SHARE-seqV2 data on [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207308) As an example, we can download the species mixing ATAC SRA record by fasterq-dump -A SRR19912835 --split-files -p This will generate two fastq files: SRR19912835_1.fastq and SRR19912835_2.fastq The read header looks like:\ head -4 SRR19912835_1.fastq\ @SRR19912835.1 A01389:111:H2Y5KDMXY:1:1101:1127:1000_R1.003,R2.032,R3.081,P1.06 length=50\ GGGCTACACAGAGAAACCCTGTCTCGAAAAACAAACAAAACAAAACAAAA\ +SRR19912835.1 A01389:111:H2Y5KDMXY:1:1101:1127:1000_R1.003,R2.032,R3.081,P1.06 length=50\ FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:\ FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: Run these lines to modify the header and convert the format to be compatable with SHARE-seq pipeline. 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
