FW: help with wiggle track display
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Hello, I need help with this track.. I am not able to get it to show up on Gbrowse.. and Im not sure what I need to change.. Hoping to get some idea.. J Hello, I know there are multiple posts about problems with individual wiggle track displays.. but I seem to be stuck in this as well.. I have the Conservation Score files from UCSC and I am trying to upload them on Gbrowse. The files look like this.. As you can see, not all positions have scores. Hence there are multiple places in the same file that have the “fixedStep chrom=Chr18 start=XXXXXX step=1” fixedStep chrom=Chr18 start=28760 step=1 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.003 0.010 0.015 0.020 0.023 0.026 0.028 0.029 0.029 0.030 0.029 fixedStep chrom=Chr18 start=31859 step=1 0.073 0.103 0.151 0.182 0.256 0.375 0.571 0.656 0.712 0.841 0.894 0.929 0.943 0.953 0.969 0.981 0.986 0.988 0.989 0.988 0.986 0.980 0.971 0.966 0.954 0.936 …. So I added the line only at the head of each file(irrespective of how many times it has the line fixedStep chrom=Chr18… repeated): track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100 and then ran the wiggle2gff2.pl script. I get this line in the gff3 file: ##gff-version 3 Chr18 rgd Conservation 28760 87247357 . . . Name=fixedStep;Note=fixedStep%20format;wigfile=/rgd/gbrowse2/databases/Conscore/track_001.Chr18.1293125672.wib I use the bp_seqfeature_load.pl script to load these files into the DB. But then I get a blank track(first wiggle file). No errors either. Where am I going wrong? Am I supposed to add the line: “track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100“ each time the line fixedStep chrom=Chr18.. repeats itself in the file? Here is the image:
And here is the configuration : [TEST_WIG] feature = Conservation glyph = wiggle_xyplot key = first wiggle file category = DETAILS:Annotated Variants Thanks, Pushkala Jayaraman Programmer/Analyst Rat Genome Database Human and Molecular Genetics Center Medical College of Wisconsin Email: [hidden email] Work: 414-955-2229 www.rgd.mcw.edu ------------------------------------------------------------------------------ Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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In reply to this post by pjayaraman
Hi Pushkala,
I'm not sure the GBrowse wiggle converter script supports multiple "fixedStep" lines in a single wiggle file. I've never seen that in a wiggle file before (though I admittedly have limited experience with them). If you trim those out but otherwise leave the file the same, does it work (though no doubt with screwed up coordinates)? Perhaps you'll need to split these into separate files. Scott On Tue, Dec 28, 2010 at 11:14 AM, Jayaraman, Pushkala <[hidden email]> wrote:
-- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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In reply to this post by Scott Cain
Thanks Scott, Ill try this.. there isn’t just two “fixedStep headings.. Each chromosome file has atleast 10-20 of those headings.. Pushkala Jayaraman Programmer/Analyst Rat Genome Database Human and Molecular Genetics Center Medical College of Wisconsin Email: [hidden email] Work: 414-955-2229 www.rgd.mcw.edu From: Scott Cain [mailto:[hidden email]] Hi Pushkala, On Tue, Dec 28, 2010 at 11:14 AM, Jayaraman, Pushkala <[hidden email]> wrote: Hello, I need help with this track.. I am not able to get it to show up on Gbrowse.. and Im not sure what I need to change.. Hoping to get some idea.. J Hello, I know there are multiple posts about problems with individual wiggle track displays.. but I seem to be stuck in this as well.. I have the Conservation Score files from UCSC and I am trying to upload them on Gbrowse. The files look like this.. As you can see, not all positions have scores. Hence there are multiple places in the same file that have the “fixedStep chrom=Chr18 start=XXXXXX step=1” fixedStep chrom=Chr18 start=28760 step=1 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.003 0.010 0.015 0.020 0.023 0.026 0.028 0.029 0.029 0.030 0.029 fixedStep chrom=Chr18 start=31859 step=1 0.073 0.103 0.151 0.182 0.256 0.375 0.571 0.656 0.712 0.841 0.894 0.929 0.943 0.953 0.969 0.981 0.986 0.988 0.989 0.988 0.986 0.980 0.971 0.966 0.954 0.936 …. So I added the line only at the head of each file(irrespective of how many times it has the line fixedStep chrom=Chr18… repeated): track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100 and then ran the wiggle2gff2.pl script. I get this line in the gff3 file: ##gff-version 3 Chr18 rgd Conservation 28760 87247357 . . . Name=fixedStep;Note=fixedStep%20format;wigfile=/rgd/gbrowse2/databases/Conscore/track_001.Chr18.1293125672.wib I use the bp_seqfeature_load.pl script to load these files into the DB. But then I get a blank track(first wiggle file). No errors either. Where am I going wrong? Am I supposed to add the line: “track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100“ each time the line fixedStep chrom=Chr18.. repeats itself in the file? Here is the image: And here is the configuration : [TEST_WIG] feature = Conservation glyph = wiggle_xyplot key = first wiggle file category = DETAILS:Annotated Variants Thanks, Pushkala Jayaraman Programmer/Analyst Rat Genome Database Human and Molecular Genetics Center Medical College of Wisconsin Email: [hidden email] Work: 414-955-2229
------------------------------------------------------------------------------ Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Hi Karthik,
I just checked again on my test machine; I had Bio::Graphics 2.15 and GBrowse 2.16 installed. I then upgraded to Bio::Graphics 2.18 and GBrowse 2.17 through CPAN. The behavior exists with both old and new versions. The behavior I am seeing is the skipping of values when using a wig file as source data, compared to data stored in either Bio:DB:SeqFeature:Store or Bio:DB:BigWig databases. To test this, I load the identical data in all three data formats (gff3, wig, and bw). The wig file is converted to a .wib file using wiggle2gff3.pl and the resulting GFF3 loaded into a B:DB:SF:Store database. The data is microarray data, with data points at varying positions along the chromosome, with a span of 1 bp (start = stop). The relevant track stanza info is below. [ma_db_rsc_chip] database = cerevisiae_test feature = RSC_ChIP_ypd_244k group_on = display_name glyph = xyplot graph_type = histogram key = DB MA RSC ypd data [ma_wig_rsc_chip] database = cerevisiae_test feature = RSC_ChIP_ypd_wig glyph = wiggle_xyplot graph_type = histogram key = Wig MA RSC ypd data [RSC_ChIP_ypd_244k_bigwig:database] db_adaptor = Bio::DB::BigWig db_args = -bigwig /Users/Shared/bigwig_data/RSC_ChIP_ypd_244k.bw [RSC_ChIP_ypd_bigwig] database = RSC_ChIP_ypd_244k_bigwig feature = summary glyph = wiggle_xyplot graph_type = histogram key = bigwig MA RSC ypd data I've attached two screenshots of the behavior, one using histogram and the other using points as the graph_type. It's harder to see with a line graph, but easiest to see with the points graph. With the wig source, there are points being dropped. Under the histogram and line graphs, this has the effect of simply extending the previous value. This can be easy to miss, depending on the data density, the noisiness of the data, and the size of the window. I've done some limited spelunking into the code and played with the respective modules outside of GBrowse in my own data collection scripts. It looks like Bio::Graphics::Wiggle returns an array of score values with the array length equal to the window size, for example 5 kb window would return an array of 5000 elements. Working with variableStep data, most of these values are undef. When the glyph is rendered for a 1000 pixel wide image, it has to grab every fifth value to plot the data across that 5 kb window. Hence, it grabs a lot of undef values, along with a few defined ones. That, at least, is my simplistic interpretation of what is going on. The B:D:SF:Store and B:DB:BW modules work in a fundamentally different manner, so this behavior isn't seen. They essentially only return the defined values. If you, or someone else, could confirm this behavior, that would be great, as it would mean I'm not imagining things. I haven't gone deep enough into the code to contribute a fix, though. Tim On 12/30/10 10:37 AM, "Karthik" <[hidden email]> wrote: > >Hello Timothy >The behavior you mentioned for variable step would be a serious problem >for >us, but I don't see that in my GBrowse. For positions with no value, I >just >don't get a point in my graph. >Was this bug fixed in the latest Bio::Graphics ? Or can you recommend a >way >for me to spot the bug ? > >Thanks >Karthik >-- >View this message in context: >http://generic-model-organism-system-database.450254.n5.nabble.com/FW-help >-with-wiggle-track-display-tp3320404p3322703.html >Sent from the gmod-gbrowse mailing list archive at Nabble.com. > >-------------------------------------------------------------------------- >---- >Learn how Oracle Real Application Clusters (RAC) One Node allows customers >to consolidate database storage, standardize their database environment, >and, >should the need arise, upgrade to a full multi-node Oracle RAC database >without downtime or disruption >http://p.sf.net/sfu/oracle-sfdevnl >_______________________________________________ >Gmod-gbrowse mailing list >[hidden email] >https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ------------------------------------------------------------------------------ Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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