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Old 04-01-2012, 11:19 PM   #1
Location: bangalore,india

Join Date: Jul 2011
Posts: 41
Default Tophat for multiple files.

Hi all,

I have three fastq file for a sample. two paired end reads and a single - end read for the same.
I want to run tophat for all together. i want to know is it possible to run 3 fq files with tophat.
Or can you please suggest a way of doing it..??

Thanking you in advance
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Old 04-02-2012, 11:52 AM   #2
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

About the 15th line of the manual.

Finally, mixing paired- and single- end reads together is not supported.
And about the 60th line in the manual:

tophat [options]* <index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]
So the answer to your question is "no" and "yes".

Read the manual. It may help.
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