1_QualityFiltering_log.txt

## 07.01.2019 ##
## Step 1 - Quality control ##

# Here I use fastqc and multiqc to decide the trim and truncate parameters for "qiime dada2 denoise-paired"
# Important is that the paired reads overlap at least 20 bp

# drop all fastq files in one single folder, here /fastqc/
cd fastq
./fastqc *.fastq.gz
./multiqc .

# open the multiqc_report.html and choose appropriate --p-trunc-len-f & --p-trunc-len-r parameters
# The bbduk_trim.sh script in "1_QualityFiltering_files" is not necessary anymore. I decided to skip the bbduk quality filtering to avoid that DADA2 and the preliminary quality trimming interfer




## Old quality filtering log content ##
## Step 1 - quality filtering ##

# quality filtering using bbduk
# https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/
# http://seqanswers.com/forums/showthread.php?t=42776

# bbduk script: bbduk_trim.sh
# copy this script into the folder with your fastq files
# execute: chmod +x bbduk_trim.sh
# execute the script: ./bbduk_trim.sh
for i in `ls -1 *_R1_001.fastq.gz | sed 's/_R1_001.fastq.gz//'`
do
~/work/bbmap/bbduk.sh -Xmx1g in1=$i\_R1_001.fastq.gz in2=$i\_R2_001.fastq.gz out1=$i\_bbduk_R1_001.fastq.gz out2=$i\_bbduk_R2_001.fastq.gz qtrim=rl trimq=20  minlen=250
done

# rename bbduk fastq files bash command
# I could also use the new names, but then I would need to change my manifest file and I don't want to do that
rename 's/bbduk_//g' *