...
Now demultiplex the reads. We will do this with process_radtags from the packages STACKS.
| Code Block | ||||
|---|---|---|---|---|
| ||||
#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 |
BFrom our barcode file, we expected to have four barcoded samples in our library.
Did we get all of our samples back?
| Code Block | ||||
|---|---|---|---|---|
| ||||
cd sample_fastqs/
#look at size of our output files
ls -lh *.fq
#remove the empty *.rem.* files
rm *.rem.*
#check the number of paired end files we have
ls *.1.fq | wc -l
ls *.2.fq | wc -l
#Are the paired end files for each sample the same size?
wc -l *.fq |