Thread: Tophat error
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Old 02-18-2019, 04:53 PM   #3
fanzhen
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Location: USA

Join Date: Feb 2019
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The following is my command.
tophat2 -p 8 -r 300 -N 1 -o tophat_out /path/ref read1 read2
And I have ref.fa and Bowtie built reference in this folder.
The last line in log file is 'Generating SAM header for /path/ref'
[2019-02-18 20:27:51] Beginning TopHat run (v2.1.2)
-----------------------------------------------
[2019-02-18 20:27:51] Checking for Bowtie
Bowtie version: 2.3.4.3
[2019-02-18 20:27:51] Checking for Bowtie index files (genome)..
[2019-02-18 20:27:51] Checking for reference FASTA file
[2019-02-18 20:27:51] Generating SAM header for /path/ref
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