Re: BigWix XYPlot: Y axis scale values truncated

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Re: bigwig track rendering failure with sparse data

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Re: bigwig track rendering failure with sparse data

OK, that sounds good. An empty track is better than a scary message about failing to render for most users.

Thanks for looking into it.

From: Lincoln Stein <lincoln.stein@...<mailto:lincoln.stein@...>>
Date: Fri, 1 Apr 2011 08:38:49 -0600
To: Timothy Parnell <timothy.parnell@...<mailto:timothy.parnell@...>>
Cc:
"gmod-gbrowse@...<mailto:gmod-gbrowse@...>" <gmod-gbrowse@...<mailto:gmod-gbrowse@...>>
Subject: Re: [Gmod-gbrowse] bigwig track rendering failure with sparse data

Hi Tim,

The difference in representation between variable and fixed stepped data is that in the former case
regions that fall between annotated regions are "missing", whereas in the latter case you must give them
an explicit value, even if it is zero.

I have changed the implementation of the wiggle_xyplot and wiggle_whiskers glyphs in Bio::Graphics so
that the scale always gets drawn. This will be released in version 2.20, which I will release as soon as I'm
sure this change doesn't introduce any new bugs.

Lincoln

On Mon, Mar 21, 2011 at 1:48 PM, Timothy Parnell
<Timothy.Parnell@...<mailto:Timothy.Parnell@...>> wrote:
Hi,

I have a lab mate who is trying to visualize her genomic data with a bigwig file. The data happens to be pretty
sparse, for example, maybe a dozen positions or less with a recorded value in a 10 kb window. These tend to
fail to render. If you zoom out to 50 or 100 kb, then the track renders properly, presumably because there
are now enough data points? If there are no data points in the requested region, then we get an empty track,
as expected (no scale bars, only vertical grid lines).

So far, this seems to happen regardless whether the source file was a variableStep wig or bedGraph file.

I hadn't seen this before, but then all my data was fixedStep. I converted her sparse data to a fixedStep wig
(assigning 0 to the empty positions, of course), and the track renders beautifully as expected,
regardless of zoom level.

Is this a bug, or an unintentional side effect of the data formatting? Has anyone else seen this phenomenon?

Tim

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101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...<mailto:Renata.Musa@...>>

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Re: bigwig track rendering failure with sparse data

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Re: bigwig track rendering failure with sparse data

Actually, the error was
"Track rendering error: Timeout; Try turning off tracks or looking at a smaller region."

I see this using the chr1_step10 wig file I included earlier (uploaded and converted to bigwig), at
coordinates chrI:184,350..189,349. The chrI_Randomized file shows an empty track.

Note that I've set the details multiplier to 1. Otherwise, you could include data points outside of your
view and preclude seeing the error.

I am using GBrowse 2.26, Bio::Graphics 2.18, and BigFile 1.04. I just noticed I was a little out of date, and
updated to Bio::Graphics 2.19 and BigFile 1.06. Still the same error.

From: Lincoln Stein <lincoln.stein@...<mailto:lincoln.stein@...>>
Date: Fri, 1 Apr 2011 09:44:29 -0600
To: Timothy Parnell <timothy.parnell@...<mailto:timothy.parnell@...>>
Cc:
"gmod-gbrowse@...<mailto:gmod-gbrowse@...>" <gmod-gbrowse@...<mailto:gmod-gbrowse@...>>
Subject: Re: [Gmod-gbrowse] bigwig track rendering failure with sparse data

Were you seeing the failing to render message? I encountered it and tracked it down to a divide-by-zero
error, but it wasn't in your bug report.

Lincoln

On Fri, Apr 1, 2011 at 11:36 AM, Timothy Parnell
<Timothy.Parnell@...<mailto:Timothy.Parnell@...>> wrote:
OK, that sounds good. An empty track is better than a scary message about failing to render for most users.

Thanks for looking into it.

From: Lincoln Stein <lincoln.stein@...<mailto:lincoln.stein@...><mailto:lincoln.stein@...<mailto:lincoln.stein@...>>>
Date: Fri, 1 Apr 2011 08:38:49 -0600
To: Timothy Parnell <timothy.parnell@...<mailto:timothy.parnell@...><mailto:timothy.parnell@...<mailto:timothy.parnell@...>>>
Cc:
"gmod-gbrowse@...<mailto:gmod-gbrowse@...><mailto:gmod-gbrowse@...<mailto:gmod-gbrowse@...>>" <gmod-gbrowse@...<mailto:gmod-gbrowse@...><mailto:gmod-gbrowse@...<mailto:gmod-gbrowse@...>>>
Subject: Re: [Gmod-gbrowse] bigwig track rendering failure with sparse data

Hi Tim,

The difference in representation between variable and fixed stepped data is that in the former case
regions that fall between annotated regions are "missing", whereas in the latter case you must give them
an explicit value, even if it is zero.

I have changed the implementation of the wiggle_xyplot and wiggle_whiskers glyphs in Bio::Graphics so
that the scale always gets drawn. This will be released in version 2.20, which I will release as soon as I'm
sure this change doesn't introduce any new bugs.

Lincoln

On Mon, Mar 21, 2011 at 1:48 PM, Timothy Parnell
<Timothy.Parnell@...<mailto:Timothy.Parnell@...><mailto:Timothy.Parnell@...<mailto:Timothy.Parnell@...>>> wrote:
Hi,

I have a lab mate who is trying to visualize her genomic data with a bigwig file. The data happens to be pretty
sparse, for example, maybe a dozen positions or less with a recorded value in a 10 kb window. These tend to
fail to render. If you zoom out to 50 or 100 kb, then the track renders properly, presumably because there
are now enough data points? If there are no data points in the requested region, then we get an empty track,
as expected (no scale bars, only vertical grid lines).

So far, this seems to happen regardless whether the source file was a variableStep wig or bedGraph file.

I hadn't seen this before, but then all my data was fixedStep. I converted her sparse data to a fixedStep wig
(assigning 0 to the empty positions, of course), and the track renders beautifully as expected,
regardless of zoom level.

Is this a bug, or an unintentional side effect of the data formatting? Has anyone else seen this phenomenon?

Tim

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514<tel:416%20673-8514>
Assistant: Renata Musa <Renata.Musa@...<mailto:Renata.Musa@...><mailto:Renata.Musa@...<mailto:Renata.Musa@...>>>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...<mailto:Renata.Musa@...>>

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Re: help with hybrid_plot glyph

Hi EChan,

This configuration is working for me (see the attached snapshot). I have
two tracks showing, one is from a BigWigSet set up with two subtracks,
each showing forward and reversed strand transcriptome data. The second
track is a hybrid_plot using the exact same two bigwig files.

For the hybrid data, I generated a GFF3 file with wigfileA and wigfileB
attributes. Here is a snippet.

##gff-version 3
chr1 data Xu_2009_YPD_mean_minus 1 230086 . . . Name=Xu_2009_YPD_mean_minus
;wigfileA=/Users/Shared/bigwig_data/Xu_2009_norm_YPD/f.bw;wigfileB=/Users/S
hared/bigwig_data/Xu_2009_norm_YPD/r_minus.bw;fasta=/Users/Shared/bigwig_da
ta/Xu_2009_norm_YPD/20100109_sequence.fasta

I should note that the bigwig file for the reverse strand has it's values
flipped (all negative data), but only for the hybrid_data track. With the
BigWigSet data the reverse strand data has positive values.

Here is my configuration.

[Xu_2009_YPD_mean_db:database]
db_adaptor    = Bio::DB::BigWigSet
db_args       = -dir /Users/Shared/bigwig_data/Xu_2009_norm_YPD
                -feature_type summary

[Xu_2009_YPD_mean]
database      = Xu_2009_YPD_mean_db
feature       = Xu_2009_norm_YPD_mean_f Xu_2009_norm_YPD_mean_r
subtrack select = Strand tag_value strand
subtrack table  = :Forward +1;
      :Reverse -1;
subtrack select labels = +1 "Forward Strand";
          -1 "Reverse Strand";
glyph         = wiggle_whiskers
min_score     = 0
max_score     = 10
height        = 50
scale         = left
clip          = 1
label         = 0
group_label   = 1
group_label_position = top
key           = Xu 2009 YPD mean transcription
category      = Microarray
citation      = Steinmetz lab YPD transcription data (Xu et al. 2009)
stored 
               in a BigWigSet.

[Xu_2009_YPD_mean_hybrid]
database      = cerevisiae_test
feature       = Xu_2009_YPD_mean_minus
glyph         = hybrid_plot
min_score     = -10
max_score     = 10
height        = 70
scale         = left
clip          = 1
bicolor_pivot = zero
pos_color     = blue
neg_color     = red
label         = 0
key           = Xu 2009 YPD mean transcription Hybrid plot
category      = Microarray
citation      = Steinmetz lab YPD transcription data (Xu et al. 2009)
stored 
               in a BigWig file using the hybrid plot.

Hope this is useful to you.

On 3/30/11 4:47 PM, "EChan" <etchan@...> wrote:

>Hi,
>
>Using this thread as a guide:
>http://generic-model-organism-system-database.450254.n5.nabble.com/forward
>-and-reverse-reads-in-wiggle-xyplot-td455898.html,
>I tried playing around with the hybrid_plot glyph to put stranded
>reads overlaid on the same plot above and below 0. However, I can't
>seem to get the values from wigfileB to flip below the axis using
>flip_sign = 1 option, so the two plots just overlap each other above
>0. If I change the scores for the minus strand to be negative, the two
>plots still overlap each other, but the minus one is appropriately
>flipped, but on a separate axis (see attached screenshot). The scale
>doesn't seem to respond to my min_score and max_score values either...
>
>Does anyone have a working example of the config for the hybrid_plot
>glyph? I'm at a loss as to why it isn't working for me. I'm using
>Bio::Graphics 2.19 and GBrowse 2.26.
>
>Thanks,
>E

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Re: bigwig track rendering failure with sparse data

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Re: [Fwd: Genbank to GFF conversion]

Hi Rachita,

Since you are interested in using these data with gbrowse, I cc'ed the gbrowse mailing list.

On your first question about phases: phase only makes sense in the context of a CDS.  For all other features,
it should be undefined and thus ".".

One the other issue of non-unique IDs: unfortunately, the conversion script is at the mercy of the author of
the original genbank file; if that author uses the same identifier for multiple features, the resulting
gff3 will be flawed.

Finally, about whether this will be suitable for use with gbrowse, the best way to find out (after
validating it) is to try it . Using webgbrowse for this sort of testing would be a good idea too:

  http://webgbrowse.cgb.indiana.edu/cgi-bin/webgbrowse/uploadData

Scott

Sent from my iPad

On 2011-04-01, at 11:57 AM, "Rachita Sharma" <rachita@...> wrote:

> Hi Scott,
> 
> I used the BioPerl script for converting Genbank file to GFF and then made
> some changes by hand to get the file validated. Please let me know if the
> changes I made make sense and should be fine for using on Gbrowse. I will
> really appreciate your help on this. I am sending you three files
> attached.
> 
> sequence.gb: original Genbank file
> 
> sequence.gb.gff: GFF file converted using BioPerl script bp_genbank2gff3.pl
> 
> sequence_validated.gff: Manually edited the above GFF file to fix to 2
> types of errors related to phase and unique identifiers described below.
> This file has been validated on
> http://public.ecolihub.net/cgi-bin/validate_gff3_online/validate_gff3_online
> 
> Error Type 1: The phase information is not given so it is replaced by '.'
> for every region but CDS region needs to have a phase information (0, 1 or
> 2 - explained below). So I have assumed it to be 0 for every region (not
> sure what should be selected out of the three). Is that a good idea?
> 
> Error Type 2: The identifiers created for every region are not unique and
> sometimes the ID-parent pair does not match so I had to get rid of the
> duplicate IDs everywhere.
> 
> Best Regards,
> 
> Rachita
> <sequence.gb>
> <sequence.gb.gff>
> <sequence_validated.gff>

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Work in the phytozome site

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Re: Work in the phytozome site

Orit,

You should probably direct this question to the phytoozome developers, not the Gbrowse mail list:

http://www.phytozome.net/contact.php

chris

On Apr 2, 2011, at 11:18 AM, Orit Shaul wrote:

> Dear help team,
> 
> I am trying to look in the phytozome site for the current data about the following chlamidomonas protein:
> MAASATGLLPIADVLQQIEALVQVLPLCTDTQEAPCREDPTSARGVAIYTQNSDVVCTSDILLPGFNMLPRWLLGAVYLLFLLYLFAGVAIASDMFMDGIMNICAITKIYKRKNEKGETIYVKEPVWNWVVANITLMALGTSSPEIMLSLVEALLTLGKPAGELGPSCIAGSAAYNFLMLRVYVVTAAWSIWAYIWMLIVYVYWTPNEVTLAEAFLTLGFFVLMVLTAWIVDKQPWKKNNKIISRSDPEAPAALPPPSVTAIVVSPAPEQAPGEAPVRTHAHYRHILAARQRHAAAAHRRLPGAHGEGGDTELQLGSGGHAYGDVVVPADPTKEQVMFRSRAYAFLESAGTARVAVTRVAPEGGSLDHPLRVHYRTEDGDAVAGLDYEAREGTLHFAPGEAYKYVEVRIIDDDMTEPDVHFSIVLTGADAPNGAGREVLVAQERVRVTIVDDDDAGVIGFELPDYEVAFNEKRTFAEVTLVRRRGADGRVTVDYETQDLSAVAGDDYVAAKGTVVFESGEKSARVRLQLLQSFVPEAHKALQLVLSNPEGGAELGKRSACKVTLVRRQFTLMPGAATAAGQKEGLELGNGSIKLVGGAEGGAGSDKGEGEGEEFNLWSAWREQIVSVFSPDEPDEGEVVSWAGLMLQYINITWKLVLFILVPPAEWKGGYPCFFAALGSIVGIVYLVNEAGSLFGCIIGLKEVMVGVSIVAVGTSLPDTLASRIAAVKDPDADAAIGNITGSNGVNVFLGLGLPWAVCSVYYHVRGEKYVTPGGDLEFAVMLYAILGGCGIFILAVAR
 YFGGELGGTKLRQYSIAGLLTVLWLLYLILSGLRAYGNI
> 
> 
> I get the following page:
> http://www.phytozome.net/cgi-bin/gbrowse/chlamy/?enable=UserBlast;ref=chromosome_11;start=2143480;end=2151856
> 
> However, despite prolonged and frutrating efforts I did not find how to get the actual nucleotide
sequence of the gene (including the regions predicted to be introns and exons). 
> 
> In addition, when I try to search for homologs of a certain protein and select all plants to blast in, I
cannot enter a protein sequence but only a gene name.
> 
> I will greatly appreciate a rapid help,
> 
> Thanks in advance,
> 
> Orit Shaul
> 
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