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Coverage track not working

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Coverage track not working

Zipixx

Hi,

I am working with two databases in my configuration file and need to display coverage tracks for both of them.
One works fine, the other does not. When using feature = match and glyph = segments however, the correct data is shown.

The track definitions for databases rnaseqall and ovarysam:

#This coverage track works
[READ_COVERAGE]
feature                 = coverage
glyph                   = wiggle_xyplot
database             = rnaseqall
height                  = 50
fgcolor                 = black
bicolor_pivot       = 20
pos_color             = royalblue
neg_color             = red
key                     = Coverage from RNA-Seq
citation                = RNA-Seq reads combined from all developmental stages.
category                = RNA-Seq

#This track does not work correctly. A scale with and a few non-matching peeks are shown.
[READ_COVERAGE_OVARY]
feature                 = coverage
glyph                   = wiggle_xyplot
database                = ovarysam
height                  = 50
fgcolor                 = black
bicolor_pivot           = 20
pos_color               = royalblue
neg_color               = red
key                     = Coverage ovary
citation                = RNA-Seq reads combined from all developmental stages.
category                = RNA-Seq

#Correct data is shown
[Reads]
feature        = match
glyph          = segments
database       = ovarysam
draw_target    = 1
show_mismatch  = 1
mismatch_color = red
bgcolor        = royalblue
fgcolor        = black
height         = 5
label density  = 50
feature_limit  = 5000
bump           = fast
connector      = solid
key            = RNA-Seq reads match ovary
category       = Experimental Data

 

Is there a method to verify the bam files are correct?
What could be causing the coverage track to be wrong?

Best Regards
Stefan Pfeiffer

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Re: Coverage track not working

Scott Cain
Hi Stefan,

I know that there can be problems associated with sampling the bam data when drawing coverage plots. Have you tried zooming in and out to see if the coverage plot changes to look more "right".  Similarly, have you tried opening the bam file in other software like IGV to see if it looks right? 

Scott


On Mon, May 8, 2017 at 11:59 AM, Stefan Pfeiffer <[hidden email]> wrote:

Hi,

I am working with two databases in my configuration file and need to display coverage tracks for both of them.
One works fine, the other does not. When using feature = match and glyph = segments however, the correct data is shown.

The track definitions for databases rnaseqall and ovarysam:

#This coverage track works
[READ_COVERAGE]
feature                 = coverage
glyph                   = wiggle_xyplot
database             = rnaseqall
height                  = 50
fgcolor                 = black
bicolor_pivot       = 20
pos_color             = royalblue
neg_color             = red
key                     = Coverage from RNA-Seq
citation                = RNA-Seq reads combined from all developmental stages.
category                = RNA-Seq

#This track does not work correctly. A scale with and a few non-matching peeks are shown.
[READ_COVERAGE_OVARY]
feature                 = coverage
glyph                   = wiggle_xyplot
database                = ovarysam
height                  = 50
fgcolor                 = black
bicolor_pivot           = 20
pos_color               = royalblue
neg_color               = red
key                     = Coverage ovary
citation                = RNA-Seq reads combined from all developmental stages.
category                = RNA-Seq

#Correct data is shown
[Reads]
feature        = match
glyph          = segments
database       = ovarysam
draw_target    = 1
show_mismatch  = 1
mismatch_color = red
bgcolor        = royalblue
fgcolor        = black
height         = 5
label density  = 50
feature_limit  = 5000
bump           = fast
connector      = solid
key            = RNA-Seq reads match ovary
category       = Experimental Data

 

Is there a method to verify the bam files are correct?
What could be causing the coverage track to be wrong?

Best Regards
Stefan Pfeiffer

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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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