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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