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#The resulting files are labled with their barcode combinations and a *tr0 suffix ls -l A*tr0 ls -l B*tr0 #How many did we get? ls -l A*tr0 | wc -l ls -l B*tr0 | wc -l #Looking back at our barcodes, does this make sense? #Which sample does B_GAAGTT_R1_ACCA.tr0 come from? #search for a line in the barcode file with both the barcodes grep TGGT barcode_data.tsv | grep GAAGTT #MCNA13 #Why search for TGGT instead of ACCA? # |
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#make a directory to put the resulting sample fastq files intomkdir 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
Check the results:
check results
#how many barcode combinations did we have?cat barcodes_Lib1.tsv | wc -l #how many r1 and r2 fastq files did we output (ignore the 'rem' files)ls sample_fastqs/*AGCGAC.1.fqls sample_fastqs/*AGCGAC.1.fq #are our paired end files still the same length?cat sample_CATAT-AGCGAC.1.fq | wc -l...
#The ligation barcode on 3Illbc was TGGT, but was then read as ACCA, so that's what shows up in the read
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