Re: segments glyph - poss bug

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Re: segments glyph - poss bug

Simon McGowan-3
Hi,

As suggested below, I added the -split_splices option to the conf file in
our GBrowse2 db (v2.08), and the splits in the reads (introns) are indeed
now being shown as a line. However, I think there is a bug in the segments
glyph to do with showing the stranded'ness of the split read.

In the first screenshot, before the -split_splices option was applied, the
two reads in a pair are shown correctly as arrows in opposite orientations.
In the second screenshot after using -split_splices, both reads in the pair
are now shown as reads in the same orientation.

Regards, Simon
--

Computational Biology Research Group
University of Oxford  OX3 9DS
www.compbio.ox.ac.uk

On 11/02/2010 17:06, Lincoln Stein wrote:

> Hi Mat,
>
> This should work.
>
> Open the Bio::DB::Sam adaptor with the option "-split_splices 1", e.g;
>
> [bamtest:database]
> db_adaptor    = Bio::DB::Sam
> db_args       = -fasta /var/www/gbrowse2/databases/chr4/chr4.fa
>         -bam   /var/www/gbrowse2/databases/chr4/chr4.sorted.bam
> -split_splices 1
> search options = exact
>
> Then in the track, adjust the connector with a subroutine:
>
> [Pair]
> feature      = read_pair
> glyph        = segments
> database     = bamtest
> draw_target  = 1
> show_mismatch=1
> bgcolor      = blue
> fgcolor      = blue
> height       = 8
> label        = sub {shift->display_name}
> label density = 50
> bump         = fast
> connector    = sub {
> my $glyph = pop; return $glyph->level == 0 ? 'dashed' : 'solid';
>                 }
> maxdepth     = 2
> box_subparts = 2
> feature_limit = 500
> key          = RNA-seq HNA3
>
> The tricky bit is the connector callback, which basically interrogates whether the glyph is at the top level (a pair) or at a lower level (an intron) and chooses the connecting line appropriately. A future version of bio::graphics will have a specialized glyph for doing this.
>
> Lincoln
>
> On Thu, Feb 11, 2010 at 11:27 AM, Mat<[hidden email]<mailto:[hidden email]>>  wrote:
> Hi there!
>
> I use tophat to align paired reads, output is SAM format. Some reads
> (which do not map) will be splitted and mapped again, so in the SAM file
> there could be an entry like:
>
> 13M1245N27M,
>
> meaning that the first 13 bases map, followed by a gap of 1245bp and
> then the rest of the read maps.
>
> Gbrowse2 displays this read as a read of length 13 + 1245 + 27 basepairs
> (long bar). Is there an easy way to display those reads correctly? Like
> to connect such a splitted read by a dotted "blue" line, while paired
> reads are connected by a dotted "green" line for example?
>
> thanks!
>
> best,
>
> mat
>
> ------------------------------------------------------------------------------
> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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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
> Assistant: Renata Musa<[hidden email]<mailto:[hidden email]>>
>
> On Thu, Feb 11, 2010 at 11:27 AM, Mat<[hidden email]<mailto:[hidden email]>>  wrote:
> Hi there!
>
> I use tophat to align paired reads, output is SAM format. Some reads
> (which do not map) will be splitted and mapped again, so in the SAM file
> there could be an entry like:
>
> 13M1245N27M,
>
> meaning that the first 13 bases map, followed by a gap of 1245bp and
> then the rest of the read maps.
>
> Gbrowse2 displays this read as a read of length 13 + 1245 + 27 basepairs
> (long bar). Is there an easy way to display those reads correctly? Like
> to connect such a splitted read by a dotted "blue" line, while paired
> reads are connected by a dotted "green" line for example?
>
> thanks!
>
> best,
>
> mat
>
> ------------------------------------------------------------------------------
> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
> http://p.sf.net/sfu/solaris-dev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]<mailto:[hidden email]>
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> 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<[hidden email]<mailto:[hidden email]>>
>

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