Path to the folder on cluster: /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/lycaeides_dubois
FOLDER Sequences
barcodeGomp012.csv = template to create the barcode file
barcodeSam036_037.csv = input barcode file to parse barcodes
barcodeTemplate.csv = template for barcodes IDs for each plate well
samplesidstemp.txt = IDs of the samples which were extracted
md5sums.txt = md5 sum check for data downloaded
SUBFOLDER phixFiltering
gomp027_S8_L002_R1_001.fastq = fastq file unzipped GBS data
gomp027_S8_L002_R1_001_out.bam = bam file
gomp027_S8_L002_R1_001_out.sai = index file
gomp027_S8_L002_R1_001_out.sam = sam file
gomp027_S8_L002_R1_001_phiXfiltered.fastq = fastq file after removing phiX
sample.mapped.sam = reads that mapped to phiX genome
sample.unmapped.bam = bam file for reads that did not map to phiX (main file for analysis)
sample.unmapped.sam = reads that did not map to phiX genome
SUBFOLDER phixSeqIndex: NC_001422.fasta (phiX fasta file from NCBI), Index files: NC_001422.fasta.ann, NC_001422.fasta.pac, NC_001422.fasta.amb NC_001422.fasta.bwt NC_001422.fasta.sa, out.sai, out.sam
FOLDER Scripts
parse_barcodesLyc036037.pl = perl script to parse barcodes
parseBarcodes.sh = bash script to run the perl script above
miderrors_gomp027_S8_L002_R1_001_phiXfiltered.fastq = output of the script above
parsed_gomp027_S8_L002_R1_001_phiXfiltered.fastq = output of the script above