Page Comparison

#look at the set of barcodes included for our samples
lesscat barcodes_Lib1.tsv 


#check the reads
grep CATG Lib01_R1.fastq | head


#check where these are in our reads
grep "^TCGAT" Lib01_R1.fastq | wc -l
grep "^CGATC" Lib01_R1.fastq | wc -l
grep "^AACCA" Lib01_R1.fastq | wc -l
grep "^GCATG" Lib01_R1.fastq | wc -l

#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