Hi, I tried to convert gff3 to csv using the pen icon (I downloaded gff3 for A.th. chromosome 4 from Ensembl). Galaxy displays it fine, it has headers and 9 columns, but after converting to csv, headers are gone and so are the last three columns. Am I doing something wrong? I read in some other post that someone else converted it exactly this way and it worked for them.
Welcome, @zupls
The transformation looks Ok to me. The result is a variant of BED output with six columns.
BED is technically tab separated columns of data instead of comma separated. Which a tool/application expects to work with can vary. When using tools in Galaxy, transformation between tabular and comma separated data happens automatically in many cases, and for other cases when a tool is “pickier”, try transforming directly first.
Here is my test history if you want to compare: https://usegalaxy.org/u/jen-galaxyproject/h/test-gff3-to-csv
Hope that helps!