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. 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:

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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


    _____________________________________________________________
    The Galaxy User list should be used for the discussion of
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    at usegalaxy.org <http://usegalaxy.org/>.  Please keep all
    replies on the list by
    using "reply all" in your mail client.  For discussion of
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    <http://lists.bx.psu.edu/listinfo/galaxy-dev>

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--
Jennifer Jackson
http://usegalaxy.org <http://usegalaxy.org/>
http://galaxyproject.org/__Support <http://galaxyproject.org/Support>

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 /jen@bx.psu.edu/* wrote:

From: Jennifer Jackson <jen@bx.psu.edu>
Subject: Re: [galaxy-user] BED to BAM conversion in Galaxy
To: "shamsher jagat" <kanwarjag@gmail.com>
Cc: galaxy-user@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 <jen@bx.psu.edu
<http://us.mc1147.mail.yahoo.com/mc/compose?to=jen@bx.psu.edu>
 > <mailto:jen@bx.psu.edu
<http://us.mc1147.mail.yahoo.com/mc/compose?to=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
 >
 >
 > _____________________________________________________________
 > 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>
 >
 > 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://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/

Now when I run the same files in the main Galaxy server it gave me following errors, Do you have any suggestion how these same files will be working ion Develop server but not on main server using same steps.

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-

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 <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


   ______________________________**______________________________**_

   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/__**Supporthttp://galaxyproject.org/__Support< http://galaxyproject.org/**Support http://galaxyproject.org/Support>

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/**Support http://galaxyproject.org/Support