Tophat2 runs nicely (6 hours) up to the step "joining segment hits". But this step (single core process, named "long_spanning_reads") is running now for almost one week.
data: 454-sequencing reads up to 500 nucleotides long probably containing a lot of exon-exon junctions.
Tophat version 2.0.0
Bowtie version: 2.0.0.6
here is the command:
tophat2 -p 12 -o tophat_out genome 454_data.fastq.gz
Does anyone has an idea what could cause this? Or maybe someone knows which parameter can be adjusted to reduce the time for this step.
Thanks
data: 454-sequencing reads up to 500 nucleotides long probably containing a lot of exon-exon junctions.
Tophat version 2.0.0
Bowtie version: 2.0.0.6
here is the command:
tophat2 -p 12 -o tophat_out genome 454_data.fastq.gz
Does anyone has an idea what could cause this? Or maybe someone knows which parameter can be adjusted to reduce the time for this step.
Thanks
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