|
|
| Line 1: |
Line 1: |
| 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. | | This page is no longer maintained. |
| | |
| ==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]
| |
| | |
| ''Is multiwig functionality available for custom tracks''
| |
| *[https://lists.soe.ucsc.edu/pipermail/genome/2010-December/024476.html 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 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 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 https://lists.soe.ucsc.edu/pipermail/genome/2011-January/024860.html]
| |
| | |
| ==Genome-Mirror==
| |
| | |
| | |
| | |
| [[Category:FAQs]]
| |
| [[Category:Browser QA]]
| |
