filelog_cluster

Path to the folder on cluster: /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/lycaeides_dubois

FOLDER Sequences

1. barcodeGomp012.csv = template to create the barcode file

2. barcodeSam036_037.csv = input barcode file to parse barcodes

3. barcodeTemplate.csv = template for barcodes IDs for each plate well

4. samplesidstemp.txt = IDs of the samples which were extracted

5. md5sums.txt = md5 sum check for data downloaded

SUBFOLDER phixFiltering

1. gomp027_S8_L002_R1_001.fastq = fastq file unzipped GBS data

2. gomp027_S8_L002_R1_001_out.bam = bam file

3. gomp027_S8_L002_R1_001_out.sai = index file

4. gomp027_S8_L002_R1_001_out.sam = sam file

5. gomp027_S8_L002_R1_001_phiXfiltered.fastq = fastq file after removing phiX

6. sample.mapped.sam = reads that mapped to phiX genome

7. sample.unmapped.bam = bam file for reads that did not map to phiX (main file for analysis)

8. sample.unmapped.sam = reads that did not map to phiX genome

   1. 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

• 1. parse_barcodesLyc036037.pl = perl script to parse barcodes

  2. parseBarcodes.sh = bash script to run the perl script above

  3. miderrors_gomp027_S8_L002_R1_001_phiXfiltered.fastq = output of the script above

  4. parsed_gomp027_S8_L002_R1_001_phiXfiltered.fastq = output of the script above