Question: Wig/BedGraph-to-bigwig converter doesn't recognize my bedGraph file - why?
0
gravatar for palle.serup
5 months ago by
palle.serup0 wrote:

Hi,

Am new to Galaxy but has successfully converted a number of downloaded Wig files to bigWig format.

When trying to do the same with bedGraph files downloaded from GEO database the files are not recognised by the converter. To me the files look ok when I check them out in a text editor.

Does anyone else have this problem - and has anyone had it and solved it?

Thanks! Palle

ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 5 months ago by palle.serup0
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k

Thanks! It was indeed datatype that should be changed from "customtrack" to "bedgraph". Works well now.

ADD REPLYlink written 5 months ago by palle.serup0
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