Processing ddRAD Quality check the reads
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#run cutadapt without any adapter sequences to cut, but with a PHRED quality cutoff of 30
#(a PHRED score of 30 indicates an expected error rate of 1/1000)
cutadapt --pair-filter=any -q 30 -o Lib01_R1_qced.fastq -p Lib01_R2_qced.fastq Lib01_R1.fastq Lib01_R2.fastq
#now rerun FastQC to see how it worked
mkdir qced_Fastqc_Restults
fastqc -o qced_Fastqc_Restults/ -f fastq Lib01_R*_qced.fastq
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Demultiplexing
Now demultiplex the reads. We will do this with process_radtags from the packages STACKS.
We expect to have
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#look at the set of barcodes included for our samples less barcodes_Lib1.tsv #make a directory to put the resulting sample fastq files into mkdir sample_fastqs #look at the documentation for process_radtags ./process_radtags -h #execute the command to process the rad data ./process_radtags -i 'fastq' -1 Lib01_R1.fastq -2 Lib01_R2.fastq -o ./sample_fastqs/ -b barcodes_Lib1.tsv --inline_index -e 'nlaIII' -r --disable_rad_check |