Frequently asked mailing list questions

This page is intended to be a collection of previously answered questions on the Genome and Genome-Mirror mailing lists that are useful for answering repeat questions.

Genome

If a user is looking for human or mouse genome updates, point them to:

• http://www.genomereference.org

To report errors in the human or mouse assemblies:

• Report a Genome Issue

For users looking for help identifying effects of their novel SNPs, send them to (thanks Angie):

• SeattleSeqAnnotation

I have a list of Gene Symbols and I would like to get corresponding sequences for them.

• http://www.soe.ucsc.edu/pipermail/genome/2007-April/013248.html

Sharing custom tracks

• sessions vs. constructing URLs, with or without using big* tracks

Help me create a Custom Track

• ...with shades of grey.
  • http://www.soe.ucsc.edu/pipermail/genome/2007-April/013185.html
• ...with
  • http://www.cse.ucsc.edu/pipermail/genome/2006-July/011100.html
  • http://www.cse.ucsc.edu/pipermail/genome/2006-September/011672.html
  • http://www.cse.ucsc.edu/pipermail/genome/2006-September/011712.html
  • http://www.cse.ucsc.edu/pipermail/genome/2006-December/012312.html
  • http://www.cse.ucsc.edu/pipermail/genome/2006-February/009847.html
  • http://www.cse.ucsc.edu/pipermail/genome/2005-October/008822.html

Is there a size limit for custom tracks?

• FW: custom track 100 MB size limit? (resend after partial bounce)

How do I find non-protein-coding genes?

• tRNA genes and not coding regions for tRNA related proteins?
• question: non-protein coding genes

I have a list of identifiers, how do I find the coordinates?

• physical positions of multiple genes

Format of chain, chainLink and net tables

• Question on net format

How do I get a table of restriction enzymes?

• Restriction enzyme track not on table browser?

Note that the utility findCutters is better than oligoMatch: oligoMatch has no good way of finding AsuI (G'GnC_C). It's possible but it would need to be run four times: GGACC, GGCCC, GGGCC, GGTCC and the output combined. findCutters does it all in one command.

GO

• All KGs that have a particular GO id
• Cow genes for a GO id

How do I find orthologous genes (using TransMap)

• Genome coordinates

How do I find telomeres and centromeres?

• Use the gap table in the Table Browser
• Filter on centromere, telomere, and heterochromatin

Questions about SNPs?

• Angie SNP mega-answer

Instructions for downloading jksrc

• http://lists.soe.ucsc.edu/pipermail/genome/2010-September/023598.html

I want to compare species A with species B

• http://lists.soe.ucsc.edu/pipermail/genome/2007-September/014719.html

To tell a user we would be willing to add a permanent custom track

• http://redmine.soe.ucsc.edu/issues/1543#note-10

Is multiwig functionality available for custom tracks

• https://lists.soe.ucsc.edu/pipermail/genome/2010-December/024476.html

Why do some gene have startCodon = stopCodon (thickStart = thickEnd)?

• https://lists.soe.ucsc.edu/pipermail/genome/2011-January/024741.html

How do I get a list of SNPs that correspond to my gene?

• https://lists.soe.ucsc.edu/pipermail/genome/2006-December/012343.html

How do I cross-reference UCSC gene names to RefSeq gene names?

• https://lists.soe.ucsc.edu/pipermail/genome/2011-January/024860.html