This is what I followed:
1. Upload the Bed file (60) > Text manipulation Add column –add this value 0; iterate –no will give file 73 2. 73 > Txt manipulation – cut > c1,c2,c3,c4,c6,c5 and delimited by tab- give file 74 3. 74> pencil icon> change data type – tabular – file 74 4. Txt manipulation- Convert all white spaces to tab – 75 5. *Condense consecutive characters- don’t find this option- I am using Dev. Galaxy version Is it somehow possible this option in develop option* 6. Change file type – BED file 75 7. Pencil> edit attribute col 5 for score- file 75 8. Run MACS from NGS peak calling- I have shared my history with you please (http://test.g2.bx.psu.edu/root) How we can annotate the genes corresponding to peaks. Thanks On Fri, Sep 30, 2011 at 7:08 AM, Jennifer Jackson <j...@bx.psu.edu> wrote: > 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- >> >> chr172402772422661PDWAAXX10070**6:4:19:6952:18071- >> >> 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 >> <mailto: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 >> >> >> ______________________________**______________________________**_ >> >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org <http://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<http://lists.bx.psu.edu/__listinfo/galaxy-dev> >> >> >> <http://lists.bx.psu.edu/**listinfo/galaxy-dev<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/ >> >> >> -- >> Jennifer Jackson >> http://usegalaxy.org <http://usegalaxy.org/> >> http://galaxyproject.org/__**Support<http://galaxyproject.org/__Support>< >> http://galaxyproject.org/**Support <http://galaxyproject.org/Support>> >> >> >> > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/**Support <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: http://lists.bx.psu.edu/
