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Force Not to Ignore Repeats in UCSC Table Browser

I have a list of official gene symbols, each gene symbol repeats several times. Ex: AATK AATK AATK AATK

I want to output some things from UCSC's table browser, but I would like the same things repeated for every gene symbol. So for every row of AATK, to give me the same information again and again (saving me time and coding to repeat).

UCSC automatically ignores repeats and gives me 1 row of info per unique gene symbol.

Any way to turn that feature off?

Thanks!

ucsc
• 1,493 views • link
written by mgru • mgru

1 answer

you don't want to do this. You want to get the regular output of the UCSC and the use something like join with your data.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Will join repeat lines? Ie, UCSC gives multiple transcripts per gene. So I assume join would read the first, join correctly but ignore the second? Would you be able to give an example? Below would be an example of my info (secondary info) and UCSC results - 2 matrices.

Ex: UCSC Results 

Col1-Transcript Col2-GeneName
Transcript1 AATK
Transcript2 AATK

Table to be joined

Col1-GeneName Col2-SecondaryInfo
AATK   A
AATK   B
AATK   C
AATK   D

Hopeful output after Join (or something else?)

  Col1-GeneName Col2-GeneName Col3-Transcript Col4-SecondaryInfo
AATK   AATK   Transcript1   A
AATK   AATK   Transcript2   A
AATK   AATK   Transcript1   B
AATK   AATK   Transcript2   B
AATK   AATK   Transcript1   C
AATK   AATK   Transcript2   C
AATK   AATK   Transcript1   D
AATK   AATK   Transcript2   D
• 1 views • link
written by mgru • mgru

Will join repeat lines?

just try, show us the command line, we'll help you if you get some problems. Hint: both files must be sorted on the common key.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks! Had a couple of errors to be honest (parentheses, dash, upper case) despite sort on common key, but it did work!

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written by mgru • mgru

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