Roberto’s Noreboock: FastQC of libraries with additional WGBS.

The results seems like before, with low Qval at the last positions.
Example of library 0501_R1_001_fastq.gz
/home/roberto/Pictures/Screenshot from 2019-05-03 14-31-08.png

Using this data, Trimming is running with conditions:
java -jar /home/Apps/trimmomatic/Trimmomatic-0.38/trimmomatic-0.38.jar PE -phred33 /home/Data_MeOH/Seq_data/0501_R1_001.fastq.gz /home/Data_MeOH/Seq_data/0501_R2_001.fastq.gz 0501_R1_001_paired.fastq.gz 0501_R1_001_unpaired.fastq.gz 0501_R2_001_paired.fastq.gz 0501_R2_001_unpaired.fastq.gz ILLUMINACLIP:TrueSeq3-PE.fa:2:30:10 LEADING:30 TRAILING:30 SLIDINGWINDOW:4:20

I did not consider the min-length option. Last time, considering MINLENGTH:100 was not good. It reduces from 58 million of reads to 35 million…

fastQC before trimming (this library has not the Additional 25% of Seqs)
/home/roberto/Pictures/Screenshot from 2019-05-03 14-37-56.png

After trimming, the result was:
/home/roberto/Pictures/Screenshot from 2019-05-03 14-40-04.png

For this reason, the MINLENGTH is not used.