Dear Sir/Madam,
Recently your Bowtie2 for paired-end reads analysis on Galaxy Europe platfrorm does not work. We wonder if you could fix it, thanks.
Have a nice weekend.
Best regards,
Chen Huiping
University Hospital of Iceland
Can you be a bit more specific please or, if possible, submit a bug report directly from the Galaxy dataset?
Hi @huiping
Maybe I can help until @wm75 is back.
The screenshot is showing that there are not any datasets in the history with the datatype formats that this tool is expecting to process.
Expand the datasets that you expected to be listed there – what is the current assigned datatype? Does this need to be adjusted?
You can use the pencil icon autodetect function to redetect the datatype. You can also uncompress directly. In general, letting Galaxy detect and assign the datatype format for common types works best!
The Mapping tutorial here can also help!
Please let us know if this helps or not! You can share back more screenshots or share the history and let us know which of the datasets you want to map with, and we can try to help with more specifics. 
Also, this tool along with a few others has recently been changed to work with paired-end data only if that data is arranged as a so-called paired collection. From your screenshot it looks as if you have regular separate datasets for fw and rv reads, but judging from the number of datasets in your history your analysis could profit greatly from using collections. If you’ve never used them, you might want to check out this tutorial although the user interface around collections has changed lately and iss not exactly like shown in this material any more.
If, for now, you prefer to keep on working with separate datasets as you did so far, you can always switch to the previous version of bowtie2 as shown in the screenshot below.
Cheers,
Wolfgang
1 Like
I appreciate it