je-demultiplex-illu does not handle UMI correctly
our IT department provides the je-demultiplex-illu tool in the galaxy suite (toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex_illu/je_demultiplex_illu/1.0)
It has been working great, but in the newest sequence data I got UMIs have been included at the start of the reads. When I activate the UMI option they are correctly removed from the reads, but not added into the headers. The IT department has informed me that the same issue exists in the console version. I already have a workaround by using your Je-Clip tool separately, I just wanted to let you know that the Je-demultiplex-illu tool is not handling the UMIs correctly (i.e. like the Je-Clip tool).
best regards and thank you for developing the tool, it has made my live much easier :) Mark
-- Mark Heron (Ph.D. Student) Soeding Lab (Protein Bioinformatics & Computational Biology) Gene Center, University of Munich (LMU) Feodor-Lynen-Strasse 25 81377 Muenchen, Germany