Trimmomatic Not Trimming Ends Off

Question

[rob234king]

I'm using Trimmomatic on gzipped paired files but the trailing low quality ends are not being trimmed?? I've done fastqc before and after and there is no removal of the trailing end poor quality reads and there are a lot. Any suggestions on what I'm missing from this comand would be appreciated.

java -jar trimmomatic-0.30.jar PE -threads 20 -phred33 /home/data/rking/MappingProject1/rawReads/A6_R1.fastq.gz /home/data/rking/MappingProject1/rawReads/A6_R2.fastq.gz /home/data/rking/MappingProject1/rawReads/A6_R1_trim15paired.fastq /home/data/rking/MappingProject1/rawReads/A6_R1_trim15unpaired.fastq /home/data/rking/MappingProject1/rawReads/A6_R2_trim15paired.fastq /home/data/rking/MappingProject1/rawReads/A6_R2_trim15unpaired.fastq TRAILING:15 MINLEN:36

[Biojl]

Could you show some reads before and after using trimmomatic?

[Istvan Albert]

as Biojl puts it show a read that you think should have been trimmed but hasn't

Answer 1

[rob234king]

Solved it just using wrong phred set at 33 when should have been 64. Thanks

[Ashutosh Pandey]

Thanks for the update. I usually convert all my reads from phred+64 to phred+33 before doing any preprocessing. Most of the pre and post alignment tools including SNP callers use phred+33 as default.

Link: Convert Illumina reads to Sanger score

[rob234king]

Scarred me, I've checked and after mapping using bowtie2 its 33 encoded output but I did not set the option, do you know if it detects which phred score is used as it does not say which is default?