Brand new to using Tophat so I tried running the test_data from the site to check my installations of Bowtie and Tophat. Tophat starts to work, but then stops.
root@kc-bio-bsb319debian:/home/bldf2b/Desktop/test_data# tophat -r 20 test_ref reads_1.fq reads_2.fq
[Fri Dec 11 16:03:43 2009] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Fri Dec 11 16:03:43 2009] Preparing output location ./tophat_out/
[Fri Dec 11 16:03:43 2009] Checking for Bowtie index files
[Fri Dec 11 16:03:43 2009] Checking for reference FASTA file
[Fri Dec 11 16:03:43 2009] Checking for Bowtie
Bowtie version: 0.11.3.0
[Fri Dec 11 16:03:43 2009] Checking reads
seed length: 75bp
format: fastq
quality scale: --phred33-quals
root@kc-bio-bsb319debian:/home/bldf2b/Desktop/test_data#
Any ideas? Thanks.
root@kc-bio-bsb319debian:/home/bldf2b/Desktop/test_data# tophat -r 20 test_ref reads_1.fq reads_2.fq
[Fri Dec 11 16:03:43 2009] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Fri Dec 11 16:03:43 2009] Preparing output location ./tophat_out/
[Fri Dec 11 16:03:43 2009] Checking for Bowtie index files
[Fri Dec 11 16:03:43 2009] Checking for reference FASTA file
[Fri Dec 11 16:03:43 2009] Checking for Bowtie
Bowtie version: 0.11.3.0
[Fri Dec 11 16:03:43 2009] Checking reads
seed length: 75bp
format: fastq
quality scale: --phred33-quals
root@kc-bio-bsb319debian:/home/bldf2b/Desktop/test_data#
Any ideas? Thanks.
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