Performed some rudimentary data analysis on the new, demultiplexed data downloaded earlier today:
2112_lane1_ACAGTG_L001_R1_001.fastq.gz
2112_lane1_ACAGTG_L001_R1_002.fastq.gz
2112_lane1_ATCACG_L001_R1_001.fastq.gz
2112_lane1_ATCACG_L001_R1_002.fastq.gz
2112_lane1_ATCACG_L001_R1_003.fastq.gz
2112_lane1_CAGATC_L001_R1_001.fastq.gz
2112_lane1_CAGATC_L001_R1_002.fastq.gz
2112_lane1_CAGATC_L001_R1_003.fastq.gz
2112_lane1_GCCAAT_L001_R1_001.fastq.gz
2112_lane1_GCCAAT_L001_R1_002.fastq.gz
2112_lane1_TGACCA_L001_R1_001.fastq.gz
2112_lane1_TTAGGC_L001_R1_001.fastq.gz
2112_lane1_TTAGGC_L001_R1_002.fastq.gz
Compared total amount of data (in gigabytes) generated from each index. The commands below send the output of the ‘ls -l’ command to awk. Awk sums the file sizes, found in the 5th field ($5) of the ‘ls -l’ command, then prints the sum, divided by 1024^3 to convert from bytes to gigabytes.
Index: ACAGTG
$ls -l 2112_lane1_AC* | awk '{sum += $5} END {print sum/1024/1024/1024}'
1.49652
Index: ATCACG
$ls -l 2112_lane1_AT* | awk '{sum += $5} END {print sum/1024/1024/1024}'
3.02269
Index: CAGATC
$ls -l 2112_lane1_CA* | awk '{sum += $5} END {print sum/1024/1024/1024}'
3.49797
Index: GCCAAT
$ls -l 2112_lane1_GC* | awk '{sum += $5} END {print sum/1024/1024/1024}'
2.21379
Index: TGACCA
$ls -l 2112_lane1_TG* | awk '{sum += $5} END {print sum/1024/1024/1024}'
0.687374
Index: TTAGGC
$ls -l 2112_lane1_TT* | awk '{sum += $5} END {print sum/1024/1024/1024}'
2.28902
Ran FASTQC on the following files downloaded earlier today. The FASTQC command is below. This command runs FASTQC in a for loop over any files that begin with “2212_lane2_C” or “2212_lane2_G” and outputs the analyses to the Arabidopsis folder on Eagle:
$for file in /Volumes/nightingales/C_virginica/2112_lane1_[ATCG]*; do fastqc "$file" --outdir=/Volumes/Eagle/Arabidopsis/; done
From within the Eagle/Arabidopsis folder, I renamed the FASTQC output files to prepend today’s date:
$for file in 2112_lane1_[ATCG]*; do mv "$file" "20150413_$file"; done
Then, I unzipped the .zip files generated by FASTQC in order to have access to the images, to eliminate the need for screen shots for display in this notebook entry:
$for file in 20150413_2112_lane1_[ATCG]*.zip; do unzip "$file"; done
The unzip output retained the old naming scheme, so I renamed the unzipped folders:
$for file in 2112_lane1_[ATCG]*; do mv "$file" "20150413_$file"; done
The FASTQC results are linked below:
20150413_2112_lane1_ACAGTG_L001_R1_001_fastqc.html
20150413_2112_lane1_ACAGTG_L001_R1_002_fastqc.html
20150413_2112_lane1_ATCACG_L001_R1_001_fastqc.html
20150413_2112_lane1_ATCACG_L001_R1_002_fastqc.html
20150413_2112_lane1_ATCACG_L001_R1_003_fastqc.html
20150413_2112_lane1_CAGATC_L001_R1_001_fastqc.html
20150413_2112_lane1_CAGATC_L001_R1_002_fastqc.html
20150413_2112_lane1_CAGATC_L001_R1_003_fastqc.html
20150413_2112_lane1_GCCAAT_L001_R1_001_fastqc.html
20150413_2112_lane1_GCCAAT_L001_R1_002_fastqc.html
20150413_2112_lane1_TGACCA_L001_R1_001_fastqc.html
20150413_2112_lane1_TTAGGC_L001_R1_001_fastqc.html
20150413_2112_lane1_TTAGGC_L001_R1_002_fastqc.html