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Old 01-01-2015, 07:53 AM   #4
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,060

Can you provide the full command you are using (example above seems to be truncated, obfuscate names if you don't want to provide specifics)?

Are you using latest tophat? Are you able to run TopHat with just the -G option without providing reads (so the transcriptome index can be pre-built?)

From TopHat manual

For example, in order to just prepare the transcriptome index files for a specific annotation, an initial, single TopHat run could be invoked like this:
tophat -G known_genes.gtf \
--transcriptome-index=transcriptome_data/known \
In this example TopHat will create the transcriptome_data directory in the current directory (if it doesn't exist already) containing files known.gff, known.fa, known.fa.tlst, known.fa.ver and the known.* Bowtie index files. Then for subsequent TopHat runs with the same genome and known transcripts but different reads, TopHat will no longer spend time building the transcriptome index because it can use the previously built transcriptome index files, so the -G option is no longer needed (however using it again will not force TopHat to rebuild the transcriptome index files if they are already present and with the matching version)
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