Frequently asked mailing list questions: Difference between revisions

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== ENCODE ==
== ENCODE ==


" 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 ?
=== 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]
 
"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/9689]
*[http://redmine.soe.ucsc.edu/issues/9656]
*[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 ?




Revision as of 06:18, 5 December 2012

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:

To report errors in the human or mouse assemblies:

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

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

Questions

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

Sharing custom tracks

Help me create a Custom Track

Is there a size limit for custom tracks?

How do I find non-protein-coding genes?

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

Format of chain, chainLink and net tables

How do I get a table of restriction enzymes?

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

How do I find orthologous genes (using TransMap)

How do I find telomeres and centromeres?


Questions about SNPs?

Instructions for downloading jksrc

I want to compare species A with species B

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

Is multiwig functionality available for custom tracks

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

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

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

Genome-Mirror

ENCODE

Helpful resources

"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 ?"

" 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 ?
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