Help with Summary Statistics

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Help with Summary Statistics

D. A. Cowart
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Re: Help with Summary Statistics

Peter Cock
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Summary Statistics

Dominique Cowart
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Re: Summary Statistics

Björn Grüning-2
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Re: Summary Statistics

Jen Hillman-Jackson
In reply to this post by Dominique Cowart
Hi Dominique,

There are a few ways to do this.

If you have the data in fasta format in your history already, skip converting to fasta-> tabular and just use that with the tool "FASTA manipulation -> Compute sequence length". Then run the statistics tool on the output.

Or, if this is the format you have to start with (tabular), the tool "Text Manipulation -> Compute" can be used with the option "length(c2)" to generate the length of column 2. Adjust the "c2" portion as needed if this is not your complete file or if you had to do extra manipulations to isolate these columns (potentially skip those steps and use the earlier file).

Thanks!

Jen
Galaxy team

ps. This mailing list has moved to Galaxy Biostar and will be closing soon. Please join us there! Here is how to get set up: https://wiki.galaxyproject.org/Support/Biostar

On 5/23/14 4:29 AM, Dominique Cowart wrote:

Hello,


I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been divided into columns:

>HD4AU5D01BHBCQC    TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
>HD4AU5D01A093MC    TCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT


I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available
via Galaxy?

Thank you in advance,


Dominique Cowart






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___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

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/

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Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: Summary Statistics

graham etherington (TSL)
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