getting gene labels to show in custom tracks
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David Nelson
Nov 2, 2017, 3:13:30 PM11/2/17
to gen...@soe.ucsc.edu
Dear Help,
I have been able to get coordinates uploaded as tracks for cytochrome P450 genes and pseudogenes in one region of elephant scaffold 99 (screenshot). However, the labels in my BED file do not show up on the browser. How can I get the labels to show? (using Firefox 56.0.2) on a MacBook Pro OS 10.9.5--
David R. Nelson
Professor
Dept. of Microbiology, Immunology and Biochemistry
858 Madison Ave. Suite G01
University of Tennessee
Memphis TN 38163
(901) 448-8303 phone
(901) 448-7360 fax
dne...@uthsc.edu
Professor
Dept. of Microbiology, Immunology and Biochemistry
858 Madison Ave. Suite G01
University of Tennessee
Memphis TN 38163
(901) 448-8303 phone
(901) 448-7360 fax
dne...@uthsc.edu
Cath Tyner
Nov 2, 2017, 5:05:35 PM11/2/17
to David Nelson, UCSC Genome Browser Public Help Forum
Hello David,
Thank you for contacting the UCSC Genome Browser support team. It looks like you are trying to load a BED4 file (chrom, start, stop, name). From the following help page, you can see examples of how to format a bed file:
Below is the format you currently have:
browser position sca99: 3715363-5052564track name="BED track" description="CYP2ABFGST cluster" visibility=2sca99 3938230-3941840 CYP2T1Psca99 3953388-3959546 CYP2F1Psca99 4040029-4040124 CYP2FxP
Which should be edited to be yourFile.bed:
browser position sca99 3715362 5052564track name="BED track" description="CYP2ABFGST cluster" visibility=2sca99 3938230 3941840 CYP2T1Psca99 3953388 3959546 CYP2F1Psca99 4040029 4040124 CYP2FxP
Note that I removed the " - " dash between columns 2 and 3 to convert to "BED" format.
I also converted your "browser position" line from "positional" to "BED" format.
The "positional" format is written like this:
sca99:3938230-3941840
and denotes a different start position than the BED format (BED counting starts from 0, positional counting starts from 1).
sca99 3938230 3941840
The differences of these two formats is worth taking the time to understand,
and are described in detail in this blog post, see "Table 1":
Once you have your bed file formatted correctly, you can set your custom track view to "full" to see the names at the left of the browser, or you can set the browser to "pack" view to see the names directly next the the annotation within the browser for each item, as seen in this session.
You may also want to check for potential issues in your BED file, such as a data violation of chrom end being larger than chrom start.
Please respond to this list if you have further questions, and please always feel free to search our mailing list archives for related posts.
Thank you for contacting the UCSC Genome Browser support team.
Please send new and follow-up questions to one of our mailing lists below:
* Confidential/private help: Email
genom...@soe.ucsc.eduEnjoy,
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Cath Tyner
Nov 2, 2017, 5:34:44 PM11/2/17
to David Nelson, UCSC Genome Browser Public Help Forum
Correction:
>You may also want to check for potential issues in your BED file, such as a data violation of chrom end being larger than chrom start.
I meant to say:
chrom start being larger than chrom end (I found one such line in your example file).
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