Hi all,
I've been trying to trim up some Illumina Hiseq 2x150 single indexed paired-end data using trimmomatic.jar PE. However after using trimmomatic, ~50% of my raw reads are thrown out. I was wondering if there was a way to potentially reduce the Q score to try and recover some of these reads. I've been using the following as my parameters:
>trimmomatic.jar PE RL04_R1_001.fastq.gz RL04_R2_001.fastq.gz ts_04_1p.fq.gz ts_04_1up.fq.gz ts_04_2p.fq.gz ts_04_2up.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36
Any help would be gratefully appreciated
You can play with the parameter SLIDINGWINDOW:4:15
- in this 4 means the size of sliding window
- and 15 is the average quality score of the sliding window
* importantly, you might want to include the -phred33 flag before you want to change the quality parameters. Trimmomatic do not detect the phred quality encodings and take phred64 as default. All new illumina score are encoded in phred33 format. May be this can cause you reads to drop.
- In general, reducing quality will just increase the uncertainty in the data. You might be careful if you change the quality parameter in your reads.
Abhijeet Singh Thanks for the response! I thought that -phred33 was the default but its good to know it isn't. I'll play around with the SLIDINGWINDOW and see if I can recover some of the reads.
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