Question: Tophat2, Strand-Specific And Genes.Gtf
gravatar for GPR
6.2 years ago by
GPR310 wrote:

Hello, I have been running Tophat2 for a while and haven't had issues with it until now that my input is a paired-end, strand-specific data set. I run Tophat2 indicating strand specificity (--library-type=fr-firststrand), without the -G genes.gtf option and everything goes well. However, Tophat2 crashes when starting to map left reads if I include the -G option. Can somebody comment on whether this is a TopHat2 bug? Otherwise: are the --library-type and -G options mutually incompatible? Thanks, G

tophat2 • 2.6k views
ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 6.2 years ago by GPR310

perhaps you should explain what you mean by tophat crashing

ADD REPLYlink written 6.2 years ago by Istvan Albert ♦♦ 80k

It stops running. When I inspect the run.log file, all I see is that it made it to aligning left reads.

ADD REPLYlink written 6.2 years ago by GPR310

may be you ran out of memory/processing power.

ADD REPLYlink written 6.2 years ago by biorepine1.4k

Yep, I thought about this, since it has happened to us in the past with a less powerful server. However, we have our disk space 50% full only, and 128 GB of ram. I have been running several TopHat jobs with no problem previously with no problem. Thanks for the suggestion though.

ADD REPLYlink written 6.2 years ago by GPR310
gravatar for Rohit
6.1 years ago by
Rohit1.3k wrote:

I think I had the same problem. If I am not wrong, it must have exited showing an error at -G, next error will be at --transcript-index. The solution is the order of the parameters you are giving.

Follow this order -

tophat -G path/gene.gff3 --transcriptome-index path/transcript-index-name path/genome-bowtie-index 1.fastq 2.fastq



ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Rohit1.3k
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