I am attempting to use the NGS mapping tool BWA-mem. I have uploaded my reference genome, in addition to my first and second files in fastqsanger format. When I click the drop down menu to select both the first and second set of reads, only my second file is coming up in the drop down menu. I have attempted to delete and re-upload the first file multiple times and nothing seems to be helping. When I manually type in the field name it says it cannot find the file. Does anyone have any suggestions as to why this is happening?
It may be that the .fastqsanger database assignment was not made for the tool-form missing dataset?
The link below shows how to assign database to datasets for tools to recognized inputs. The section immediately below has help for confirming that the data is in fact in .fastqsanger format before assigning this directly (otherwise use the FastQ Groomer tool to adjust quality scores):
Best, Jen, Galaxy team