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Wei-HD

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Join Date: Oct 2009

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#1

Data txt file

01-21-2010, 04:17 AM

Hi All,

I want to ask a very basic question concerning the input file format for Tophat and Cufflinks.

My data file is txt file and Fastq format. But where I should start for using Tophat, should I just upload the txt file?

Thanks in advance!

Wei

Last edited by Wei-HD; 01-21-2010, 04:20 AM.
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Xi Wang

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#2

01-21-2010, 05:10 AM

Fastq format is ok for tophat. Refer to the tophat manual. Cufflinks uses the output of tophat as input.

Xi Wang
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Wei-HD

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01-21-2010, 05:21 AM

Thanks Xi!
I read the manual, the test_data has .fq suffix, could I use .txt file directly?
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Jonathan

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#4

01-21-2010, 05:29 AM

Usually, yes. If it complains, just rename the file and rerun.
-Jonathan
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