Hello Biomart users,
I've been testing BioMart 0.8 for my organization but running into some
difficulty. I hope you can guide me in the right direction. I'm new to
BioMart so please forgive me if my questions are mundane.
I've setup a single mysql table with the contents of a BED file (chrom,
chromStart, chromEnd, Name, etc). When I connect BioMart to this mysql
table the column names become chrom_101, chromStart_101, ect. This requires
me to do a lot of manual renaming across potentially hundreds of tables (or
perhaps eventually write a script to automate this). Is that typical and
can it be changed?
It appears that 0.8 does not support wildcard searches ('ABC%' in the name
field for example). Is that correct? Also related to searching some of my
names include commas and pluses (the text 'ABC,+' for example). Both the
comma and plus appear to prevent searching. in other words if I search for
'ABC,+' in the name column I return no results even though I have a 'ABC,+'
row in my table. If there is a way to escape these characters I have not
found it. This is especially frustrating considering that I cannot do a
wildcard search.
Last, is it true that at this time 0.8 only supports downloads as TSV? I
believe 0.7 included XLS. Is this still in progress?
Lastly, are these issues I'm having related to 0.8 being a release
candidate? Should I be using 0.7 instead. Thank you so much for your time.
Jayson
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