INFO @ Tue, 04 Oct 2011 14:56:21: # ARGUMENTS LIST: # name = MACS_in_Galaxy # format = BED # ChIP-seq file = /galaxy/main_database/files/003/068/dataset_3068865.dat # control file = /galaxy/main_database/files/003/068/dataset_3068668.dat # effective genome size = 2.70e+09 # tag size = 25 # band width = 300 # model fold = 30 # pvalue cutoff = 5.00e-02 # Ranges for calculating regional lambda are : peak_region,1000,5000,10000 INFO @ Tue, 04 Oct 2011 14:56:21: #1 read tag files... INFO @ Tue, 04 Oct 2011 14:56:21: #1 read treatment tags... INFO @ Tue, 04 Oct 2011 14:56:32: 1000000 INFO @ Tue, 04 Oct 2011 14:56:44: 2000000 INFO @ Tue, 04 Oct 2011 14:56:55: 3000000 INFO @ Tue, 04 Oct 2011 14:57:06: 4000000 INFO @ Tue, 04 Oct 2011 14:57:19: 5000000 INFO @ Tue, 04 Oct 2011 14:57:30: 6000000 INFO @ Tue, 04 Oct 2011 14:57:41: 7000000 INFO @ Tue, 04 Oct 2011 14:57:52: 8000000 INFO @ Tue, 04 Oct 2011 14:58:03: 9000000 INFO @ Tue, 04 Oct 2011 14:58:15: 10000000 INFO @ Tue, 04 Oct 2011 14:58:26: 11000000 INFO @ Tue, 04 Oct 2011 14:58:37: 12000000 INFO @ Tue, 04 Oct 2011 14:58:49: #1.2 read input tags... Traceback (most recent call last): File "/home/g2main/linux2.6-x86_64/bin/macs", line 273, in main() File "/home/g2main/linux2.6-x86_64/bin/macs", line 57, in main (treat, control) = load_tag_files_options (options) File "/home/g2main/linux2.6-x86_64/bin/macs", line 256, in load_tag_files_options control = options.build(open2(options.cfile, gzip_flag=options.gzip_flag)) File "/home/g2main/linux2.6-x86_64/lib/python2.6/MACS/IO/__init__.py", line 1063, in build_fwtrack (chromosome,fpos,strand) = self.__fw_parse_line(thisline) File "/home/g2main/linux2.6-x86_64/lib/python2.6/MACS/IO/__init__.py", line 1102, in __fw_parse_line raise self.StrandFormatError(thisline,thisfields[5]) MACS.IO.StrandFormatError: 'Strand information can not be recognized in this line: "chr1\t10093\t10093\t10292\t61PDWAAXX100706:4:82:5766:21319

I can share this history if required please.

Thanks.

On Mon, Oct 3, 2011 at 3:58 PM, shamsher jagat <kanwarjag@gmail.com> wrote:

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 <jen@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-

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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