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

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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

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):

$ 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 |
+------------------------+--------------------+--------+---------------------+---------------------+----------+

To save a user's session to a file:

• From a shell prompt, enter a command similar to the following:

$ hgsql -h genome-centdb -Ne "select contents from namedSessionDb where userName like 'Gunnar%' and sessionName='2Lfullgenom'" hgcentral > gunnarSession

• The session can then be restored from this file on the hgSession page in the "Restore Settings" section

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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

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