Hi, I am trying to use MACS among your NGS peak-calling tools, but I can't work it out. I have ELAND files; what should I specify as a file format when uploading them? There is no ELAND format in the 'upload file' window. If I choose BED as a format, after running MACS I get no results (empty) and a Strand Format Error message, although I am sure the strand information in my ELAND file is correct (9th column, F or R). If I choose TABULAR, instead, my files are not even visualized in the MACS dropdown menu. Is this a problem of input file format, as I suspect? Thanks, -- Claudia Cattoglio, PhD Tjian Lab University of California, Berkeley Department of Molecular & Cell Biology 16 Barker Hall # 3204 Berkeley, CA 94720-3204 phone: (510) 643-3762
Claudia;
I am trying to use MACS among your NGS peak-calling tools, but I can't work it out.
I have ELAND files; what should I specify as a file format when uploading them? There is no ELAND format in the 'upload file' window. If I choose BED as a format, after running MACS I get no results (empty) and a Strand Format Error message, although I am sure the strand information in my ELAND file is correct (9th column, F or R). If I choose TABULAR, instead, my files are not even visualized in the MACS dropdown menu.
Is this a problem of input file format, as I suspect?
I don't make much direct experience with Eland format, but have not seen support for it in Galaxy. My suggestion would be to convert your Eland output into BED, and then proceed. Taking a quick look, here is one perl script that may work for you: http://www.pangloss.com/wiki/Solexa/ElandExport2BED Hope this helps, Brad
Hi Brad, I had updated my galaxy instance and tried to set up a trackster for BED wiggle format file. I was wondering that after a long hours of waiting I can just see a message that is loading data.... I am not sure what is happening. I used a BED wiggle file with four fields, and following the instructions in the url http://bitbucket.org/galaxy/galaxy-central/wiki/Visualization. Please let me know your comments. thanks in advance, Vipin T S On 27 April 2010 15:23, Brad Chapman <chapmanb@50mail.com> wrote:
Claudia;
I am trying to use MACS among your NGS peak-calling tools, but I can't work it out.
I have ELAND files; what should I specify as a file format when uploading them? There is no ELAND format in the 'upload file' window. If I choose BED as a format, after running MACS I get no results (empty) and a Strand Format Error message, although I am sure the strand information in my ELAND file is correct (9th column, F or R). If I choose TABULAR, instead, my files are not even visualized in the MACS dropdown menu.
Is this a problem of input file format, as I suspect?
I don't make much direct experience with Eland format, but have not seen support for it in Galaxy. My suggestion would be to convert your Eland output into BED, and then proceed. Taking a quick look, here is one perl script that may work for you:
http://www.pangloss.com/wiki/Solexa/ElandExport2BED
Hope this helps, Brad _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Claudia, I've added support for ELAND and ELANDMULTI formats to Galaxy and proper support for these to MACS in rev 3701:b633d836ce07, which is now available on the test server. It will be available on the main server the next time it is updated. Thanks for using Galaxy, Dan On Apr 26, 2010, at 5:55 PM, Claudia Cattoglio wrote:
Hi,
I am trying to use MACS among your NGS peak-calling tools, but I can't work it out.
I have ELAND files; what should I specify as a file format when uploading them? There is no ELAND format in the 'upload file' window. If I choose BED as a format, after running MACS I get no results (empty) and a Strand Format Error message, although I am sure the strand information in my ELAND file is correct (9th column, F or R). If I choose TABULAR, instead, my files are not even visualized in the MACS dropdown menu.
Is this a problem of input file format, as I suspect?
Thanks,
-- Claudia Cattoglio, PhD
Tjian Lab University of California, Berkeley Department of Molecular & Cell Biology 16 Barker Hall # 3204 Berkeley, CA 94720-3204
phone: (510) 643-3762 _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Thank you Dan, any idea of when is the next main server update? On Tue, 27 Apr 2010 11:08:24 -0400, Daniel Blankenberg wrote: Hi Claudia, I've added support for ELAND and ELANDMULTI formats to Galaxy and proper support for these to MACS in rev 3701:b633d836ce07, which is now available on the test server. It will be available on the main server the next time it is updated. Thanks for using Galaxy, Dan On Apr 26, 2010, at 5:55 PM, Claudia Cattoglio wrote: Hi, I am trying to use MACS among your NGS peak-calling tools, but I can't work it out. I have ELAND files; what should I specify as a file format when uploading them? There is no ELAND format in the 'upload file' window. If I choose BED as a format, after running MACS I get no results (empty) and a Strand Format Error message, although I am sure the strand information in my ELAND file is correct (9th column, F or R). If I choose TABULAR, instead, my files are not even visualized in the MACS dropdown menu. Is this a problem of input file format, as I suspect? Thanks, -- Claudia Cattoglio, PhD Tjian Lab University of California, Berkeley Department of Molecular & Cell Biology 16 Barker Hall # 3204 Berkeley, CA 94720-3204 phone: (510) 643-3762 _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu [1] http://lists.bx.psu.edu/listinfo/galaxy-dev -- Claudia Cattoglio, PhD Tjian Lab University of California, Berkeley Department of Molecular & Cell Biology 16 Barker Hall # 3204 Berkeley, CA 94720-2321 phone: (510) 643-3762 Links: ------ [1] mailto:galaxy-dev@lists.bx.psu.edu
participants (4)
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Brad Chapman -
Claudia Cattoglio -
Daniel Blankenberg -
Vipin TS