qseq to fastq with or without Illumina chastity filter


# 1) Convert reads from qseq format to fastq format without filter

# Log on to Oscar
ssh oscar

# Go to your working folder
mkdir data/working
cd data/working

# Setup the path of the input files in qseq format, which are created by Illumina software (Bustard or OLB)
QSEQ=/path/to/qseq/files

# Setup the lane ID you are going to work with
LANE=s_1

# Convert the read 1 files from qseq format to fastq format without filter (all reads will converted)
cat
${QSEQ}/${LANE}_1_*qseq.txt | perl /gpfs/runtime/bioinfo/bin/qseq2fastq_all.pl > ${LANE}_1_sequence.txt

# Convert the read 2 files from qseq format to fastq format without filter (all reads will converted)
cat
${QSEQ}/${LANE}_2_*qseq.txt | perl /gpfs/runtime/bioinfo/bin/qseq2fastq_all.pl > ${LANE}_2_sequence.txt

# 2) Convert reads from qseq format to fastq format with the default Illumina filter

# Log on to Oscar
ssh oscar

# Go to your working folder
mkdir data/working
cd data/working

# Setup the path of the input files in qseq format, which are created by Illumina software (Bustard or OLB)
QSEQ=/path/to/qseq/files

# Setup the lane ID you are going to work with
LANE=s_1

# Convert the read 1 files from qseq format to fastq format without filter (all reads will converted)
cat
${QSEQ}/${LANE}_1_*qseq.txt | perl /gpfs/runtime/bioinfo/bin/qseq2fastq.pl > ${LANE}_1_sequence.txt

# Convert the read 2 files from qseq format to fastq format without filter (all reads will converted)
cat
${QSEQ}/${LANE}_2_*qseq.txt | perl /gpfs/runtime/bioinfo/bin/qseq2fastq.pl > ${LANE}_2_sequence.txt

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