Hello,

The format of the BED file may be a problem. To be in BED format, an
additional field is required for the "score" attribute. This would be
column 5, moving the strand out to column 6.

To do this:

1 - use "Text Manipulation->Add column" with the value "0"
note: "0" often is used to represent a NULL or undefined score value in
BED files. This field cannot be left as whitespace (two tabs), a
placeholder value must be present.

2 - then use ""Text Manipulation->Cut" and cut out the columns in the
proper BED file order, in this case "c1,c2,c3,c4,c6,c5", to swap the
last two

3 - change datatype to BED using the pencil icon/Edit attributes form

In Galaxy, many of the tools in "NGS: Peak Calling" will work with
ChIP-seq data in BED format. Having a control would be helpful, but is
not required by all tools.

Good luck with your project,

Jen
Galaxy team

On 9/29/11 9:31 PM, shamsher jagat wrote:
> Thanks Jen,
> My problem is I have ChIP-seq data where I have one Bed
> file with coordinates-
>
> chr172402772422661PDWAAXX100706:4:19:6952:18071-
>
> Then there is wig file.? Is it possible that thsi data can be analyzed
> in Galaxy/ Cistrome. I tried to use Cistrome which gav eme error message.
>
> Thanks
>
>
>
> On Wed, Sep 28, 2011 at 3:46 PM, Jennifer Jackson <jen@bx.psu.edu
> <mailto:jen@bx.psu.edu>> wrote:
>
>    Hello,
>
>    It is possible to go from SAM/BAM to BED, but not the reverse.
>    SAM/BAM files contain the actual sequence data associated with the
>    original aligned read. BED files only have the reference genome
>    location of the alignment (no read "sequence").
>
>    It is possible to extract genomic sequence based on BED coordinates,
>    but the resulting sequence would not necessarily be the same
>    sequence as in the original aligned read (any variation would be lost).
>
>    BED is very similar to Interval format, so Interval tools also work
>    with BED format. A BED file is basically a 3-12 column, tab
>    delimited file, so tools that work with Tabular data are also
>    appropriate for BED file. Note that you may need to change the
>    datatype to be interval or tab for certain tools to recognize a BED
>    file as an input.
>
>    Hopefully this helps,
>
>    Jen
>    Galaxy team
>
>
>
>
>    On 9/22/11 2:55 PM, shamsher jagat wrote:
>
>    Is it possible to use some tool in Galaxy to convert BED file to
>    Bam/
>    sam file. In other word do we have Bed tools or other option in
>    Galaxy
>
>    Thanks
>
>
>    _____________________________________________________________
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>    --
>    Jennifer Jackson
>    http://usegalaxy.org <http://usegalaxy.org/>
>    http://galaxyproject.org/__Support <http://galaxyproject.org/Support>
>
>

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
___________________________________________________________
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:

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