https://bioinformaticsonline.com/snippets/view/41025/to-convert-just-one-specific-read-group-to-fastq? https://bioinformaticsonline.com/snippets/view/41025/to-convert-just-one-specific-read-group-to-fastq Fri, 14 Feb 2020 03:35:22 -0600 https://bioinformaticsonline.com/snippets/view/41025/to-convert-just-one-specific-read-group-to-fastq # Stop script on error. set -uex # The SRR BioProject number for the sequencing data. PROJECT=PRJNA257197 # The number of datasets to subselect from the project. N=5 # Get the project run information. esearch -db sra -query $PROJECT | efetch -format runinfo > runinfo.txt # Select the first N elements. Keep only valid SRR numbers. cat runinfo.txt | cut -f 1 -d , | grep SRR | head -$N > selected.txt # Store the data in the reads folder. mkdir -p reads # Download the SRR data for each cat selected.txt | parallel fastq-dump -O reads -X 1000 --split-files {} # Create a directory for bam files mkdir -p bam # Generate a separate BAM file for each SAMPLE. cat selected.txt | parallel "picard FastqToSam F1=reads/{}_1.fastq F2=reads/{}_1.fastq O=bam/{}.bam RG=GROUP-{} LB=LIB-{} SM=SAMPLE_{} QUIET=true 2>> log.txt" # Merge all the BAM files into one. samtools merge -f all.bam bam/*.bam # Investigate the readgroups in the header. echo "" echo "SAM file header:" samtools view -H all.bam echo "" echo "Number of alignments with read group: GROUP-SRR1972919" samtools view -c -r GROUP-SRR1972919 all.bam # Reverting the process is to extract reads, tagged with readgroups to paired files. samtools fastq -t -1 all1.fq -2 all2.fq all.bam # To convert just one specific read group. samtools view -r GROUP-SRR1972919 all.bam | samtools fastq -t -1 all_SRR1972919_1.fq -2 all_SRR1972919_2fq -]]> Rahul Nayak