View source for 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 http://www.genomereference.org]
To report errors in the human or mouse assemblies:
*[http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/ReportAnIssue.shtml Report a Genome Issue]
For users looking for help identifying effects of their novel SNPs, send them to (thanks Angie):
*[http://gvs.gs.washington.edu/SeattleSeqAnnotation/ 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 http://www.soe.ucsc.edu/pipermail/genome/2007-April/013248.html]

Sharing custom tracks
*[https://lists.soe.ucsc.edu/pipermail/genome/2010-April/022110.html 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 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-July/011100.html]
**[http://www.cse.ucsc.edu/pipermail/genome/2006-September/011672.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-September/011712.html]
**[http://www.cse.ucsc.edu/pipermail/genome/2006-December/012312.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/2006-February/009847.html]
**[http://www.cse.ucsc.edu/pipermail/genome/2005-October/008822.html http://www.cse.ucsc.edu/pipermail/genome/2005-October/008822.html]

''Is there a size limit for custom tracks?''
*[http://www.soe.ucsc.edu/pipermail/genome/2007-April/013324.html FW: custom track 100 MB size limit? (resend after partial bounce)]

''How do I find non-protein-coding genes?''
*[http://www.soe.ucsc.edu/pipermail/genome/2007-October/014924.html tRNA genes and not coding regions for tRNA related proteins?]
*[http://www.soe.ucsc.edu/pipermail/genome/2008-January/015286.html question: non-protein coding genes]

''I have a list of identifiers, how do I find the coordinates?''
*[http://www.soe.ucsc.edu/pipermail/genome/2007-May/013674.html physical positions of multiple genes]

''Format of chain, chainLink and net tables''
*[http://www.soe.ucsc.edu/pipermail/genome/2006-February/009869.html Question on net format]

''How do I get a table of restriction enzymes?''
*[http://www.soe.ucsc.edu/pipermail/genome/2006-May/010707.html 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''
*[http://www.soe.ucsc.edu/pipermail/genome/2008-June/016605.html All KGs that have a particular GO id]
*[http://www.soe.ucsc.edu/pipermail/genome/2008-June/016527.html Cow genes for a GO id]

''How do I find orthologous genes (using TransMap)''
*[http://www.soe.ucsc.edu/pipermail/genome/2008-July/016784.html Genome coordinates]

''How do I find telomeres and centromeres?''
*[http://www.soe.ucsc.edu/pipermail/genome/2006-July/011229.html Use the gap table in the Table Browser]
*[http://www.soe.ucsc.edu/pipermail/genome/2006-July/011232.html Filter on centromere, telomere, and heterochromatin]


''Questions about SNPs?''
*[http://lists.soe.ucsc.edu/pipermail/genome/2009-September/020019.html Angie SNP mega-answer ]

''Instructions for downloading jksrc''
*[http://lists.soe.ucsc.edu/pipermail/genome/2010-September/023598.html 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 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 http://redmine.soe.ucsc.edu/issues/1543#note-10]

==Genome-Mirror==



[[Category:FAQs]] 
[[Category:Browser QA]]