Thread: Tophat/Bowtie
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Old 01-12-2016, 05:34 PM   #6
GenoMax
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Join Date: Feb 2008
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Quote:
Originally Posted by TPH View Post
Hi,
Thank you so much for your kind help.
Anyway this is the output I get

@SRR057634.1 HWUSI-EAS230-R:1:2:28:1908 length=36
CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCC
+SRR057634.1 HWUSI-EAS230-R:1:2:28:1908 length=36
@AA>?;55555565555555.!-1444444441144
@SRR057634.2 HWUSI-EAS230-R:1:2:29:1475 length=36
CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCC
That means you do have read permissions on the sequence file so that is not an issue. The error you are getting is misleading.

Can you tell me where you are trying to run this? On a stand alone server/cluster? Can you look at the directory to see if tophat wrote a log file and if it has any additional clues?

This may sound arcane but can you try to change "-o tophat-tumor-out" to "-o tophat_tumor_out" (underscores instead of hyphens) and see what happens?

Last edited by GenoMax; 01-12-2016 at 05:40 PM.
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