run time with extrinsic data
Posted: Thu Nov 19, 2015 5:27 pm
Originally posted in the old forum by Marcin on 19.08.2013 - 16:47
I am trying to use Augustus with RNA-Seq data. I have normalized/cleaned my RNA-Seq with Trinity In silico Read Normalization protocol and prepared evidence file according to http://bioinf.uni-greifswald.de/augustu ... naseq.html
With these extrinsic data Augustus slowed down to the point that it will take months to complete (on 24 cores). Is it normal or did I messed with the RNA-Seq evidence data? My RNA-Seq hints gff3 file has 390 MB and 6.8 million lines. The genome is Eukaryote size is 300 Mbases in 7,000 scaffolds.
I will appreciate any input.
I am trying to use Augustus with RNA-Seq data. I have normalized/cleaned my RNA-Seq with Trinity In silico Read Normalization protocol and prepared evidence file according to http://bioinf.uni-greifswald.de/augustu ... naseq.html
With these extrinsic data Augustus slowed down to the point that it will take months to complete (on 24 cores). Is it normal or did I messed with the RNA-Seq evidence data? My RNA-Seq hints gff3 file has 390 MB and 6.8 million lines. The genome is Eukaryote size is 300 Mbases in 7,000 scaffolds.
I will appreciate any input.