Opened 3 months ago
Last modified 5 weeks ago
#1609 closed defect
Misconfiguration is causing Trimmomatic adapter trimming to be skipped when demuxing RNAseq data — at Initial Version
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | critical | Milestone: | Reggie v5.2 |
| Component: | net.sf.basedb.reggie | Keywords: | |
| Cc: |
Description
In our config file we have the following setting for the adapter trimming step:
ILLUMINACLIP:${TRIMMOMATIC_ADAPTERS}:2:30:12:1:true MINLEN:20
The ${TRIMMOMATIC_ADAPTERS} environment variable used to contain the path the a FASTA-file with the adapter sequences: /usr/local/packages/trimmomatic/0.32/adapters/TruSeq3-PE-2.fa but when we moved to the new cluster and Singularity containers the filename was lost from the variable and it was never noticed that it was missing. Trimmomatic doesn't fail but doens't do any adapter trimming either.
The configuration need to be updated to:
ILLUMINACLIP:${TRIMMOMATIC_ADAPTERS}/TruSeq3-PE-2.fa:2:30:12:1:true MINLEN:20
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