Question: Tophat2, Strand-Specific And Genes.Gtf
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gravatar for GPR
6.2 years ago by
GPR310
Mexico
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
0
gravatar for Rohit
6.1 years ago by
Rohit1.3k
California
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

Regards,

Rohit

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