bam reads color

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bam reads color

Pedrolance
Hi, 

I am still using WebApollo 1.0. 

So far I can only see the BAM reads as green, independently of their alignment direction.

<a href="http://cap.ensemblgenomes.org/Ztritici/jbrowse/?loc=11:535162..535459&amp;tracks=DNA,Annotations,Genes Wageningen,Genes Core,Zt09_YMS_18C_200rpm_01.bam&amp;highlight=" class="">http://cap.ensemblgenomes.org/Ztritici/jbrowse/?loc=11%3A535162..535459&tracks=DNA%2CAnnotations%2CGenes%20Wageningen%2CGenes%20Core%2CZt09_YMS_18C_200rpm_01.bam&highlight=

 Tried to put the following under style in the track configuration:

  color_fwd_strand: '#EC8B8B',
  color_rev_strand: '#8F8FD8’,

But nothing changed. 

Where do I need to make this configuration in order to see the different colours for read direction?

Cheers

Helder Pedro




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Re: bam reads color

nathandunn

I think the same patch should work for 1.0.  Try adding webapollo_track_style.css

/* CIGAR string "M" subfeature, indicating "alignment match" (can be a sequence match or mismatch) of aligned sequence relative to viewed sequence */
.cigarM {
height: 100%;
background-color: #1B8A99;
z-index: 8; /* rendered below most other subfeatures */
min-width: 1px;
}

.plus-cigarM {
height: 100%;
/*background-color: #898FD8;*/
background-color: indianred;
/*background-color: blue;*/
z-index: 8; /* rendered below most other subfeatures */
min-width: 1px;
}

.minus-cigarM {
height: 100%;
/*background-color: #EC8B8B;*/
background-color: royalblue;
/*background-color: red;*/
z-index: 8; /* rendered below most other subfeatures */
min-width: 1px;
}

.bam-read{
height: 5px;
background-color: #AACDDC;
z-index: 8;
}

.plus-bam-read {
height: 5px;
background-color: #EC8B8B;
z-index: 8;
}

.minus-bam-read {
height: 5px;
background-color: #898FD8;
z-index: 8;
}
From this PR:




Nathan



On Oct 26, 2017, at 6:12 AM, Helder Pedro <[hidden email]> wrote:

Hi, 

I am still using WebApollo 1.0. 

So far I can only see the BAM reads as green, independently of their alignment direction.


 Tried to put the following under style in the track configuration:

  color_fwd_strand: '#EC8B8B',
  color_rev_strand: '#8F8FD8’,

But nothing changed. 

Where do I need to make this configuration in order to see the different colours for read direction?

Cheers

Helder Pedro



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.