Hello,
I'm trying to get TopHat running but am getting the following error about not being able to find bowtie:
>>python tophat -r 20 test_ref reads_1.fq reads_2.fq
[Fri Jun 4 12:53:41 2010] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Fri Jun 4 12:53:41 2010] Preparing output location ./tophat_out/
[Fri Jun 4 12:53:41 2010] Checking for Bowtie index files
[Fri Jun 4 12:53:41 2010] Checking for reference FASTA file
[Fri Jun 4 12:53:41 2010] Checking for Bowtie
[FAILED]
Error: bowtie not found on this system
I am working on a Mac OS X machine and am unsure how to specify a "path". I usually place the program in the working directory. In this case, I have a TopHat directory where I've placed everything (the test data, the reference set, the TopHat executables, and the bowtie executables):
bed_to_juncs juncs_db test_ref.2.ebwt
bowtie library_stats test_ref.fa
bowtie-build long_spanning_reads test_ref.rev.1.ebwt
bowtie-inspect mask_sam test_ref.rev.2.ebwt
closure_juncs prep_reads tophat
contig_to_chr_coords reads_1.fq tophat_out
extract_reads reads_2.fq tophat_reports
fix_map_ordering segment_juncs
gff_juncs test_ref.1.ebwt
Any suggestions for how to get the computer to find Bowtie?
Thanks.
I'm trying to get TopHat running but am getting the following error about not being able to find bowtie:
>>python tophat -r 20 test_ref reads_1.fq reads_2.fq
[Fri Jun 4 12:53:41 2010] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Fri Jun 4 12:53:41 2010] Preparing output location ./tophat_out/
[Fri Jun 4 12:53:41 2010] Checking for Bowtie index files
[Fri Jun 4 12:53:41 2010] Checking for reference FASTA file
[Fri Jun 4 12:53:41 2010] Checking for Bowtie
[FAILED]
Error: bowtie not found on this system
I am working on a Mac OS X machine and am unsure how to specify a "path". I usually place the program in the working directory. In this case, I have a TopHat directory where I've placed everything (the test data, the reference set, the TopHat executables, and the bowtie executables):
bed_to_juncs juncs_db test_ref.2.ebwt
bowtie library_stats test_ref.fa
bowtie-build long_spanning_reads test_ref.rev.1.ebwt
bowtie-inspect mask_sam test_ref.rev.2.ebwt
closure_juncs prep_reads tophat
contig_to_chr_coords reads_1.fq tophat_out
extract_reads reads_2.fq tophat_reports
fix_map_ordering segment_juncs
gff_juncs test_ref.1.ebwt
Any suggestions for how to get the computer to find Bowtie?
Thanks.
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