I am using Flexbar on the CRS4 Orione galaxy server. This tool is very useful as it allows to define homology parameters for barcode detection/removal and adapter removal. The problem is : when I add it to my workflow it is impossible to connect it with the downstream steps !! I realized that the output appeared as TXT which seems to be the logfile, but the fastq file output is not there...!?
Any solution ?
For information, I am processing single-end illumina reads coming from a PCR library.
I know the flanking regions of my reads and need to:
- select the sequence that contain the 5' constant region (with >90%homology for the 39 first nt; 100% for the last 3nt) and remove that sequence
- remove the 3' constant sequence when it is present
Flexbars allows to do that very easily, either using the barcode tool (for the 5' region) or the adapter tool (3' region).
Thanks for your help !