I am pretty certain that I found out why mm7 is not extracting - the
database is not fully set up to use with this tool (although the
data is present). I'll add this to the list of items to adjust this
upcoming month (plus find/fix any others like it - all would be
And glad the tab file is now working. Whenever you really do have
just a tabular file - using a plain text editor is best along with
the option on the 'Get Data -> Upload File' form of '
Convert spaces to tabs:'. Excel is known to most bioinformatics
folks as a tool that it is wise to carefully screen any "text"
output from - primarily because of inserted 'hidden' or whitespace
characters (soft returns and such). Not Excel's fault, nor any other
editor's - but what you did (cycle through a plain text editor) is
one way gain clear data.
Now, that said -> never use that upload option on any file that
would contain internal spaces - such as GFF/GTF, or SAM, but for
plain text tabular, in particular strict BED, this can help clean up
stray spaces or tabs introduced. Other tools in Text manipulation
can also help for data already loaded (try cutting out the columns
you want to use, maybe after converting all whitespace to tabs
Thanks and glad you have a working solution. I missed the details of
the mm7 extract issue originally - sorry if that was confusing!
On 10/31/13 6:46 AM, Kreiling, Jill
Thank you Jen. You mentioned it may be a
formatting problem and you were able to successfully convert the
coordinates to mm8. I tried that several times yesterday and
they kept coming up in the unmapped file saying the region was
deleted from the newer build. I opened the tab deliminated text
file I created in Excel in Notepad++ and just resaved it without
changing anything. When I uploaded the new file to galaxy and
and lifted over to mm8 it worked fine. It still wouldn't pull
out genomic sequences from mm7, but it will from the new file
converted to mm8. Thank you for your help - it is very much