only display 1 strand

[Valentin Feichtenschlager]

Hello,

 

I was wondering if it is possible to only show sense or antisense strand genes in the UCSC genome browser.

 

Thank you

Valentin

 

Sent from Mail for Windows

 

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

You can use the Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables) to create two custom
tracks, one for each strand. The following Table Browser steps will help you get the positive strand
from the GENCODE Genes track for hg38.

Step 1: Configure the Table Browser

On the Table Browser and apply the following settings.

clade: mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: Genes and Gene Predictions
track: GENCODE V38
table: knownGene
region: genome
output format: custom track

Step 2: Create a filter

Next to filter; click create.

You will be taken to a new page where you can filter the genes track. For the "strand" field,
change the asterisk to a plus.

strand does match +

After making that change to the filter, click submit.

Step 3: Create a custom track

With the filter in place, click the get output on the main Table Browser page. You will then be
taken to a new page where you can get one BED record for each gene. We recommend that you
change the custom track header name to something informative, such as "Positive strand genes".

To get the genes for the negative strand, you can change the filter in Step 2 to match the minus sign.

strand does match -

We are curious why you are separating the genes from the positive and negative strands. Could
you let us know why you are trying to achieve this goal?

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

Want to share the Browser with colleagues?
Host a workshop: https://bit.ly/ucscTraining

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