filter option in UCSC browser

[Troyee Das]

Hello,

           I want to apply two filters while downloading data from Table browser.

1. cdsStart=cdsEnd and 2. txEnd-txStart>199.

Can you please guide me how to apply both the filters at the same time?

Sincerely,

Troyee Das

 

[Cath Tyner]

Hello Troyee,

Thank you for contacting the UCSC Genome Browser support team. You can use the following free-form queries to get non-coding transcripts that are longer than 199 bp in the Table Browser:

The two queries below will provide the same results, either can be used. Note the missing open and closing parenthesis in #2:

1. 

(cdsStart=cdsEnd) AND (txEnd-txStart>199)

2. 

cdsStart=cdsEnd) AND (txEnd-txStart>199

Example outout using #1 above:

#filter: ((cdsStart=cdsEnd) AND (txEnd-txStart>199))

#name txStart txEnd cdsStart cdsEnd

uc057aty.1 29553 31097 29553 29553

uc057atz.1 30266 31109 30266 30266

uc001aak.4 34553 36081 34553 34553

uc057aua.1 35244 36073 35244 35244

uc057aub.1 89294 120932 89294 89294

uc057auc.1 89550 91105 89550 89550

uc057aud.1 92229 129217 92229 92229

Also, here is a related previously answered mailing list question that you may be interested in, which shows another method for getting non-coding transcripts. 

Please respond to this list if you have further questions!

Thank you for contacting the UCSC Genome Browser support team. 

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Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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