Content-Type: multipart/alternative; boundary="----_=_NextPart_002_01CBA6AA.41D5F032" ------_=_NextPart_002_01CBA6AA.41D5F032 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hello,=20 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..=20 Hoping to get some idea.. J =20 =20 Hello,=20 I know there are multiple posts about problems with individual wiggle track displays.. but I seem to be stuck in this as well..=20 I have the Conservation Score files from UCSC and I am trying to upload them on Gbrowse.=20 =20 The files look like this..=20 As you can see, not all positions have scores. Hence there are multiple places in the same file that have the "fixedStep chrom=3DChr18 start=3DXXXXXX step=3D1" =20 fixedStep chrom=3DChr18 start=3D28760 step=3D1 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=3DChr18 start=3D31859 step=3D1 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=20 .... =20 =20 So I added the line only at the head of each file(irrespective of how many times it has the line fixedStep chrom=3DChr18... repeated): track type=3Dwiggle_0 name=3D"fixedStep" description=3D"fixedStep = format" visibility=3Dfull autoScale=3Doff viewLimits=3D0:1000 color=3D0,200,100 =20 and then ran the wiggle2gff2.pl script.=20 I get this line in the gff3 file: ##gff-version 3 =20 Chr18 rgd Conservation 28760 87247357 . . . Name=3DfixedStep;Note=3DfixedStep%20format;wigfile=3D/rgd/gbrowse2/databa= ses/C onscore/track_001.Chr18.1293125672.wib =20 =20 =20 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.=20 Where am I going wrong? =20 Am I supposed to add the line: "track type=3Dwiggle_0 name=3D"fixedStep" description=3D"fixedStep format" visibility=3Dfull autoScale=3Doff viewLimits=3D0:1000 color=3D0,200,100" each time the line fixedStep chrom=3DChr18.. repeats itself in the file? =20 Here is the image: =20 =20 =20 And here is the configuration : [TEST_WIG] feature =3D Conservation glyph =3D wiggle_xyplot key =3D first wiggle file category =3D DETAILS:Annotated Variants =20 =20 Thanks,=20 Pushkala Jayaraman Programmer/Analyst Rat Genome Database Human and Molecular Genetics Center Medical College of Wisconsin Email: pjayaraman@mcw.edu Work: 414-955-2229 www.rgd.mcw.edu =20 ------_=_NextPart_002_01CBA6AA.41D5F032 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

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=3DChr18 start=3DXXXXXX = step=3D1”

 

fixedStep = chrom=3DChr18 start=3D28760 step=3D1

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=3DChr18 start=3D31859 step=3D1

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=3DChr18… repeated):

track type=3Dwiggle_0 name=3D"fixedStep" = description=3D"fixedStep format" visibility=3Dfull = autoScale=3Doff viewLimits=3D0:1000 color=3D0,200,100

 

and then ran = the wiggle2gff2.pl script.

I get = this line in the gff3 file:

##gff-version 3

 

Chr18   rgd     = Conservation    28760   = 87247357        = .       = .       = .       = Name=3DfixedStep;Note=3DfixedStep%20format;wigfile=3D/rgd/gbrowse2/databa= ses/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=3Dwiggle_0 name=3D"fixedStep" = description=3D"fixedStep format" visibility=3Dfull = autoScale=3Doff viewLimits=3D0:1000 color=3D0,200,100“ each time = the line fixedStep chrom=3DChr18.. repeats itself in the = file?

 

Here is the image:

 

 

And here is = the configuration :

[TEST_WIG]

feature = =3D Conservation

glyph   = =3D wiggle_xyplot

key     =3D first wiggle = file

category =3D DETAILS:Annotated = Variants

 

 

Thanks, =

Pushkala = Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics = Center

Medical College of Wisconsin

Email: = pjayaraman@mcw.edu

Work: = 414-955-2229

www.rgd.mcw.edu

 

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