Hello everyone, I just signed up and wanted to say hi and also ask a question. I just installed tophat and bowtie and created a test file from my large fastq file. This test file has only ten sequences in it (40 lines total). When I run the tophat command it took a very short time and produced the following verbose and an output directory as was supposed to. My question is, in the verbose below there is a statement saying "Warning: junction database is empty!". Can anyone kindly explain what this means or perhaps refer me to a source where I could read about it more. The verbose is pasted below. Thank you for your time.
[Wed Jun 2 12:10:20 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 2 12:10:20 2010] Preparing output location ./tophat_out/
[Wed Jun 2 12:10:20 2010] Checking for Bowtie index files
[Wed Jun 2 12:10:20 2010] Checking for reference FASTA file
[Wed Jun 2 12:10:20 2010] Checking for Bowtie
Bowtie version: 0.12.5.0
[Wed Jun 2 12:10:20 2010] Checking reads
seed length: 76bp
format: fastq
quality scale: phred33 (default)
[Wed Jun 2 12:10:20 2010] Mapping reads against mm9 with Bowtie
[Wed Jun 2 12:10:53 2010] Joining segment hits
Splitting reads into 3 segments
[Wed Jun 2 12:10:53 2010] Mapping reads against mm9 with Bowtie
[Wed Jun 2 12:11:28 2010] Mapping reads against mm9 with Bowtie
[Wed Jun 2 12:12:02 2010] Mapping reads against mm9 with Bowtie
[Wed Jun 2 12:12:36 2010] Searching for junctions via segment mapping
Warning: junction database is empty!
[Wed Jun 2 12:12:36 2010] Joining segment hits
[Wed Jun 2 12:12:37 2010] Reporting output tracks
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Run complete [00:02:17 elapsed]
[Wed Jun 2 12:10:20 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Wed Jun 2 12:10:20 2010] Preparing output location ./tophat_out/
[Wed Jun 2 12:10:20 2010] Checking for Bowtie index files
[Wed Jun 2 12:10:20 2010] Checking for reference FASTA file
[Wed Jun 2 12:10:20 2010] Checking for Bowtie
Bowtie version: 0.12.5.0
[Wed Jun 2 12:10:20 2010] Checking reads
seed length: 76bp
format: fastq
quality scale: phred33 (default)
[Wed Jun 2 12:10:20 2010] Mapping reads against mm9 with Bowtie
[Wed Jun 2 12:10:53 2010] Joining segment hits
Splitting reads into 3 segments
[Wed Jun 2 12:10:53 2010] Mapping reads against mm9 with Bowtie
[Wed Jun 2 12:11:28 2010] Mapping reads against mm9 with Bowtie
[Wed Jun 2 12:12:02 2010] Mapping reads against mm9 with Bowtie
[Wed Jun 2 12:12:36 2010] Searching for junctions via segment mapping
Warning: junction database is empty!
[Wed Jun 2 12:12:36 2010] Joining segment hits
[Wed Jun 2 12:12:37 2010] Reporting output tracks
-----------------------------------------------
Run complete [00:02:17 elapsed]
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