Hello Vasu,

The score value should be "0" for each row. When adding the new column, set "Iterate?:" to the default "no".


It also looks like there may be some inconsistencies in the original file. Are you certain it is 5 columns (exactly) for every row? Including the error row reported? Some detective work to get the file in the right format is probably necessary.

Tabs are good to check. Change the filetype to tabular, run the file through the "Convert delimiters to TAB" tool using "Convert all: whitespace", next run "Condense consecutive characters" to cleanup any trailing tabs, then change the filetype back to BED and assign the score column on the "Edit Attributes" form (pencil icon).

Hopefully this helps,

Jen
Galaxy team


On 9/30/11 3:13 PM, vasu punj wrote:
Jen,
I ran the flow as you suggested, but got following error message, Do You
hav eany suggestion? I added 0 and flips the columns: Here is the few
lines of input file:
chr1    12137   12336   61R33AAXX100706:1:79:7707:9270  0       -
chr1    31542   31741   61R33AAXX100706:1:37:11341:10600        1       -
chr1    39921   40120   61R33AAXX100706:1:2:16103:17629         2       -
chr1    93213   93412   61R33AAXX100706:1:113:14396:2056        3       -
chr1    109395  109594  61R33AAXX100706:1:13:8451:9619  4       -
chr1    146854  147053  61R33AAXX100706:1:53:15558:13513        5       -

Te error message is as follow

INFO  @ Fri, 30 Sep 2011 17:59:54:
# ARGUMENTS LIST:
# name = macs_output
# format = BED
# ChIP-seq file = 
/data/CistromeAP/galaxy_database/files/000/198/dataset_198187.dat
# control file = None
# effective genome size = 2.79e+09
# band width = 300
# model fold = 10,30
# pvalue cutoff = 1.00e-05
# Small dataset will be scaled towards larger dataset.
# Range for calculating regional lambda is: 10000 bps

INFO  @ Fri, 30 Sep 2011 17:59:54: #1 read tag files...
INFO  @ Fri, 30 Sep 2011 17:59:54: #1 read treatment tags...
INFO  @ Fri, 30 Sep 2011 18:00:02:  1000000
INFO  @ Fri, 30 Sep 2011 18:00:11:  2000000
INFO  @ Fri, 30 Sep 2011 18:00:21:  3000000
INFO  @ Fri, 30 Sep 2011 18:00:30:  4000000
INFO  @ Fri, 30 Sep 2011 18:00:39:  5000000
Traceback (most recent call last):
   File "/usr/local/bin/macs14", line 358, in<module>
     main()
   File "/usr/local/bin/macs14", line 60, in main
     (treat, control) = load_tag_files_options (options)
   File "/usr/local/bin/macs14", line 330, in load_tag_files_options
     treat = tp.build_fwtrack()
   File "/usr/lib/python2.6/dist-packages/MACS14/IO/Parser.py", line 150, in 
build_fwtrack
     (chromosome,fpos,strand) = self.__fw_parse_line(thisline)
   File "/usr/lib/python2.6/dist-packages/MACS14/IO/Parser.py", line 187, in 
__fw_parse_line
     raise StrandFormatError(thisline,thisfields[5])
MACS14.IO.Parser.StrandFormatError: 'Strand information can not be recognized in this line: 
"chr2\t121859840\t121860039\t61R33AAX\t.\t5837743","5837743"'

Thanks
Vasu

--- On *Fri, 9/30/11, Jennifer Jackson /<j...@bx.psu.edu>/* wrote:


    From: Jennifer Jackson <j...@bx.psu.edu>
    Subject: Re: [galaxy-user] BED to BAM conversion in Galaxy
    To: "shamsher jagat" <kanwar...@gmail.com>
    Cc: galaxy-u...@bx.psu.edu
    Date: Friday, September 30, 2011, 9:08 AM

    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 <j...@bx.psu.edu
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=j...@bx.psu.edu>
     > <mailto:j...@bx.psu.edu
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=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
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     > <http://lists.bx.psu.edu/listinfo/galaxy-dev>
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     > To manage your subscriptions to this and other Galaxy lists,
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     >
     > --
     > Jennifer Jackson
     > http://usegalaxy.org <http://usegalaxy.org/> <http://usegalaxy.org/>
     > http://galaxyproject.org/__Support <http://galaxyproject.org/Support>
     >
     >

    --
    Jennifer Jackson
    http://usegalaxy.org <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:

    http://lists.bx.psu.edu/


--
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
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