Local genome browser (isPCR)

[Ana Carolina Tahira]

Dear UCSC team, 

I'm running the genome browser locally and using in silico PCR (isPCR), which is working fine!

However, I don't know how to configure the "target" box in the in silico PCR section. I searched in the blat help page and I didn't find it. Could you give me an orientation on how to do this!?

Best 

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[Jonathan Casper]

Hi Ana,

Thanks for writing in, and we're delighted to hear your mirror is working well!

The contents of the "target" box are determined by the records in the mariaDb database, particularly in the hgcentral table named "targetDb". Each record in that table lists a particular target for one assembly. This record, for example, lists our current "GENCODE Genes" PCR target for the hg38 human genome assembly:

> select * from targetDb where name = "hg38KgSeqV46" \G
*************************** 1. row ***************************
        name: hg38KgSeqV46
 description: GENCODE Genes
          db: hg38
    pslTable: kgTargetAli
    seqTable:
extFileTable:
     seqFile: /gbdb/hg38/targetDb/hg38KgSeqV46.2bit
    priority: 1
        time: 2024-04-05 21:56:06
    settings:

The 2bit file contains sequence for each of the sequences that the isPCR search should hunt through. kgTargetAli entry is a table in the hg38 database that lists where each of those sequences is mapped to in the hg38 assembly. There is also a corresponding entry in the hgcentral table "blatServers" that points to an untranslated gfServer set up to handle BLAT queries on that same 2bit file (we use stepSize=5 for the server).

That might be more information than you're looking for. What kind of configuration did you have in mind? Are you interested in adding more options to the list, or just in reconfiguring something already present?

Thanks,
Jonathan Casper
UCSC Genome Browser

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