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==
===Helpful Items===
----
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]
To check a user's Browser session in hgcentral:
*From a shell prompt, enter a command similar to the following (depending on the username or session name you are searching for):
<pre>$ hgsql -h genome-centdb -e "select userName,sessionName,shared,firstUse,lastUse,useCount from namedSessionDb where userName like 'Gunnar%'" hgcentral
+------------------------+--------------------+--------+---------------------+---------------------+----------+
| userName               | sessionName        | shared | firstUse            | lastUse             | useCount |
+------------------------+--------------------+--------+---------------------+---------------------+----------+
| Gunnar%20H.            | 2Lfullgenom        |      1 | 2011-07-19 23:37:37 | 2011-09-27 13:42:47 |       43 |
| Gunnar%20H.            | 2Rfullgenom        |      1 | 2011-07-20 01:42:25 | 2011-08-20 05:17:27 |       28 |
| Gunnar%20H.            | 3Lfullgenom        |      1 | 2011-07-20 03:43:01 | 2011-09-27 06:43:31 |       31 |
| Gunnar%20H.            | 3Rfullgenom        |      1 | 2011-07-19 13:22:43 | 2011-08-20 05:18:21 |       31 |
| Gunnar%20H.            | 4fullgenom         |      1 | 2011-07-20 03:49:44 | 2011-09-27 07:34:00 |       25 |
| Gunnar%20H.            | dm3cov             |      1 | 2011-07-05 17:22:22 | 2011-08-25 05:02:24 |       22 |
| Gunnar%20H.            | dm3sub             |      1 | 2011-07-19 11:12:51 | 2011-07-27 00:22:07 |        4 |
| Gunnar%20H.            | Split              |      1 | 2011-09-03 05:00:42 | 2011-09-05 08:18:29 |        4 |
| Gunnar%20H.            | Xfullgenom         |      1 | 2011-07-20 05:21:20 | 2011-09-27 07:33:21 |       23 |
| Gunnar.thor.sigurdsson | mm9_test_session_1 |      1 | 2010-09-29 03:34:38 | 2010-09-29 03:34:38 |        0 |
+------------------------+--------------------+--------+---------------------+---------------------+----------+</pre>
To save a user's session to a file:
*From a shell prompt, enter a command similar to the following:
<pre>$ hgsql -h genome-centdb -Ne "select contents from namedSessionDb where userName like 'Gunnar%' and sessionName='2Lfullgenom'" hgcentral > gunnarSession</pre>
*The session can then be restored from this file on the hgSession page in the "Restore Settings" section
----
===Questions===
''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==

== ENCODE ==

=== Helpful resources ===
*[http://encodeproject.org/ENCODE/cellTypes.html Cell Types page]
* Experiment matrix
* Track and File Search
*[http://encodeproject.org/ENCODE/pubs.html Publications page]
*[http://nature.com/ENCODE Nature microsite]

=== Questions ===

"Which cell types are used by ENCODE ?   Did XXX ENCODE track use standard ENCODE cell protocols ?   What was the ENCODE growth protocol for cell type YYY ?"
*[http://redmine.soe.ucsc.edu/issues/9689]
*[http://redmine.soe.ucsc.edu/issues/9656]

" Has transcription factor XXX been mapped by ENCODE ?   How do I find overlaps between my own ChIP-seq regions and ENCODE transcription factors ?

* What is represented by field NN in ENCODE bed files ?

* What is the difference between file XX and files XXV2 ?   Why is file XX not displayed in the browser ?

* How do I interpret an ENCODE filename ?

* How do I display ENCODE data at GEO ?


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