Thanks Jen,

My problem is I have ChIP-seq data where I have one Bed
file with  coordinates-


chr1       724027  724226  61PDWAAXX100706:4:19:6952:18071       -

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 <j...@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
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>
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