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 followINFO  @ 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
> <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
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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
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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___________________________________________________________
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
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