Frequently asked mailing list questions: Difference between revisions

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1) ''How do I display ENCODE data at GEO in the genome browser ?''
1) ''How do I display ENCODE data at GEO in the genome browser ?''
* Not by loading a custom track!  Basically all  ENCODE data at GEO data are already hosted in tracks at UCSC.  Use Track Search and enter the GEO sample accession (GSM).
* Not by loading a custom track!  Basically all  ENCODE data at GEO data are already hosted in tracks at UCSC.  Use Track Search and enter the GEO sample accession (GSM).
A great answer by Pauline is here:  http://redmine.soe.ucsc.edu/issues/10037


2) ''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 ?''
2) ''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 ?''

Revision as of 20:14, 24 January 2013

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

Questions

1) How do I display ENCODE data at GEO in the genome browser ?

  • Not by loading a custom track! Basically all ENCODE data at GEO data are already hosted in tracks at UCSC. Use Track Search and enter the GEO sample accession (GSM).

A great answer by Pauline is here: http://redmine.soe.ucsc.edu/issues/10037

2) 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 ?

  • See Cell Types page on portal. All ENCODE tracks use protocols registered on this page. Click 'Documents' link to see growth protocol. If you have further questions, contact lab that registered the protocol [1] [2]

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

  • Use ChIP-seq Experiment Matrix to show mapped TFs. Use Table Browser to intersect ENCODE Regulation Txn Factor clusters with custom track of user regions. [3]

4) What is represented by field NN in ENCODE bed files ?

  • See File Formats page for descriptions of ENCODE 'peak' file formats. See track descriptions for how scores and values were derived.

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

  • Versioned files are often revoked and so not viewable in the browser, though still available for download. Revoke status is shown in metadata (files.txt).

6) How do I extract information about an ENCODE experiment from the filename ?

  • Don't do it! Filenames have some metadata embedded, but can only be relied on to be unique. Use file metadata, available in the following places:
    • Downloads directories: files.txt file
    • Track UI: down-arrow next to subtrack
    • Track/File search
    • genome-mysql, table browser: metaDb table
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