Hello, Dan.
Please see this previously-answered mailing list question for a good
explanation of Sequence Type Number:
https://lists.soe.ucsc.edu/pipermail/genome/2011-March/025223.html
In response to your question about why exon data is not used for every gene,
exon coordinates are used for every gene. It may not always be obvious
because some genes only contain one exon while others, such as in your
example, contain multiple exons. In the case of a gene with multiple exons,
the Sequence Type Number becomes more apparent, as you noticed.
In response to your question about knowing when you need a Sequence Type
Number, the public MySql table and the Table Browser have no notion of a
Sequence Type Number - the mysql table has one row per transcript and the
Table Browser breaks out the tx{Start,End}, cds{Start,End}, strand and
exon{Starts,Ends} coordinates into a series of per-exon coords (with CDS
parts of exons clipped off).
Please contact us again at [email protected] if you have any further
questions.
---
Steve Heitner
UCSC Genome Bioinformatics Group
-----Original Message-----
From: [email protected] [mailto:[email protected]] On
Behalf Of Dan Morton
Sent: Tuesday, March 27, 2012 6:30 PM
To: [email protected]
Subject: [Genome] 3' UTR - Sequence Type Number
When downloading 3' UTR data for a particular range I get the following
results related to "uc010drt.1"
chr19 | 680714 | 680879 | uc010drt.1_utr3_0_0_chr19_680715_f
| 0 | + | 165
chr19 | 681332 | 681560 | uc010drt.1_utr3_1_0_chr19_681333_f
| 0 | + | 228
chr19 | 681649 | 683392 | uc010drt.1_utr3_2_0_chr19_681650_f
| 0 | + | 1743
I noticed the "Sequence Type Number" for this gene increments for this gene.
Indicating that exon data is used?
- Why is exon data not used for every gene and how do I know when?
After downloading and looking through the website src I discovered that this
number is related to something called extraSize and a trackQualifier.
When using the genome public mysql server how do I know when I need a
"Sequence Type Number".
I know this is a lot to ask, and helpful information will greatly
appreciated.
Thanks,
Dan
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
