5 months ago by
Check the datatype assigned to these data and adjust it to be
bedgraph. You can set this in the Upload tool (when loading new data) or reset it after (for data that is already loaded). The Upload tool is very good at autodetecting datatype, but doesn't always get it right due to small format differences, and can be overridden when the datatype in Upload is directly set ("autodetect" is not used).
Also, check the data content versus the Bedgraph specification if autodetect didn't assign this correctly. It should, and if it failed, can indicate a content problem.
Example: the extra header lines some data providers add to datasets can interfere with type detection. You might need to remove those headers for the data to be processed by tools correctly (some community tools are more flexible than others). You can remove headers before or after upload with Text Manipulation tools. GTF datasets with custom headers not being correctly autodetected as
gtf is a known (the type will fall back to the more generic
gff and sometimes even just
tabular). This is difficult to get around programmatically since the header content/format can vary so much between sources. Most tools will require that those GTF headers are removed and the datatype directly adjusted before using the data with tools. The same applies to BEDGraph and other datatypes. Using the most conservative formatting helps to avoid tool errors.
Support FAQs: https://galaxyproject.org/support >> https://galaxyproject.org/support/#getting-inputs-right
Thanks! Jen, Galaxy team