Column Join feature

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Column Join feature

bsjec
Hi,

I am analysing some RNA-seq data and have two different datasets, total RNA plus enzyme and total RNA minus enzyme. I used to type in "column join" in the "Tools" menu on the Galaxy homepage after uploaded the files in Text delimited format. Column join allowed me to join two datasets by a hinge column, in this case I would choose column 1 which would be the chromosome position. I would also be allowed to fill empty columns with a value of 1. The output would give me 3 columns, chromosome number (which both datasets shared), reads for minus enzyme, and reads for plus enzyme. The function would never reject any chromosome position with reads in one dataset and not the other. However, I cannot seem to be able to find this function anymore, and the new function "Join two datasets" seems to only give me back rows where both plus and minus datasets have reads. Does anyone else have this problem or know how I could get around it?

Regards,

Justin


----------------------------------
Justin Clarke
McDowall Laboratory
Garstang 8.52/8.51
Faculty of biological sciences
University of Leeds
Leeds
LS2 9JT
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Re: Column Join feature

Jen Hillman-Jackson
Hello Justin,

Unfortunately, this tool is no longer supported. As an alternative, you
can create a workflow to obtain the same results. It will include a few
different tools, but the intermediate datasets can be hidden and just
the results shown.

The tools in the group "Join, Subtract and Group" that remain have
options to output non-matching rows, fill in empty fields, etc. The
general idea is to run two queries - one that captures all the data from
the first file (matching and non-matching) and then the data from the
second file (non-matching, by switching the file order in the tool), and
in the end put the results together. The tool "Text Manipulation ->
Concatenate datasets" can merge files and "Filter and Sort -> Sort" can
reorganize the rows.

Once you work out the steps, use the history menu option "Extract
Workflow" to create the workflow from that start. Edit as needed, then
save and use.

Hopefully this will work out for you,

Jen
Galaxy team

On 3/6/14 3:40 AM, Justin Clarke wrote:

> Hi,
>
> I am analysing some RNA-seq data and have two different datasets, total RNA plus enzyme and total RNA minus enzyme. I used to type in "column join" in the "Tools" menu on the Galaxy homepage after uploaded the files in Text delimited format. Column join allowed me to join two datasets by a hinge column, in this case I would choose column 1 which would be the chromosome position. I would also be allowed to fill empty columns with a value of 1. The output would give me 3 columns, chromosome number (which both datasets shared), reads for minus enzyme, and reads for plus enzyme. The function would never reject any chromosome position with reads in one dataset and not the other. However, I cannot seem to be able to find this function anymore, and the new function "Join two datasets" seems to only give me back rows where both plus and minus datasets have reads. Does anyone else have this problem or know how I could get around it?
>
> Regards,
>
> Justin
>
>
> ----------------------------------
> Justin Clarke
> McDowall Laboratory
> Garstang 8.52/8.51
> Faculty of biological sciences
> University of Leeds
> Leeds
> LS2 9JT
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
>    http://galaxyproject.org/search/mailinglists/

--
Jennifer Hillman-Jackson
http://galaxyproject.org



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
http://galaxyproject.org