Tophat2, Strand-Specific And Genes.Gtf

Question

[GPR]

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

[Istvan Albert]

perhaps you should explain what you mean by tophat crashing

[GPR]

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

[biorepine]

may be you ran out of memory/processing power.

[GPR]

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.

Answer 1

[Rohit]

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