AUGUSTUS Forum

Hi Katharina, Sorry for bothering again=-= I have done the gene prediction using the script with Scipio method, which I wrote at the beginning. Unfortunately, the result looks like pretty strange==: 1. Predicted gene numbers of Scipio method (<5000) is much less than the protein numbers which I prov...

Hi Katharina, I write a python script here: L=[] #the files you need to convert for i in L: infile=open(i+'.scipio.gff','r') outfile=open(i+'.scipio.hints','w') for line in infile: outfile.write(line[:line.index('tr')]+'source=P; grp='+line[line.index('tr'):line.index('id')+2]+'_'+line[line.index('&...

Hi Katharina, I found the exonerate here (http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=Augustus.IncorporateProteins) Thanks, Best, Yafei Hi Katharina, Thanks your useful reply^^ Could you tell me what's name of the script you mentioned above is? Yafei Thanks again, BTW, are there some sc...

For my case, what do you think of the two different ways (hints from scipio.gff or from proteins)? For my understanding, all of analysis are based on scipio method, so, maybe using scipio.gff to generate hints is better? Thanks,^^,sorry for so many questions=-= Best, Yafei Hi Katharina, Thanks your ...

Hi Katharina, Thanks your useful reply^^ Could you tell me what's name of the script you mentioned above is? Yafei Thanks again, BTW, are there some scripts for directly converting this scipio.gff file to hints file in the software scripts directory? I don't think so. We have scripts to generate hin...

Moreover, for the converting, I only need to add ';source=P' at the 9th column. Right? Thanks a lot. Yafei Thanks again, BTW, are there some scripts for directly converting this scipio.gff file to hints file in the software scripts directory? If available, I add the evidence, sure. Maybe you should ...

Thanks again, BTW, are there some scripts for directly converting this scipio.gff file to hints file in the software scripts directory? If available, I add the evidence, sure. Maybe you should run both. You need to examine results in a Browser, anyway, and then you can compare: scipio genes, ab init...

Hi Katharina, if I convert the gff file to the right format, do you think the second one with right hints file is better than the first one for gene prediction? The second command will not work because the gff file is not in hints format. You can easily convert it, though. HInts format is described ...

Hi Katharina,

Thanks a lot ^^

Best,
Yafei

Hi guys, I am using the related specie's protein file to do gene prediction. According to the introduction (http://bioinf.uni-greifswald.de/augustus/binaries/tutorial/scipio.html), I built the pipeline like below: perl scipio.1.4.1.pl --blat_output=As.prot.vs.genome.psl As.fa At.gff.aa > As.scipio.y...

Hi guys, I am using optimize_augustus.pl to optimize my 'new' species. But It has been taking over six days on 24 CPU =-= importantly, the time will be out soon because I set the max running time is 6 days and 23 hours. So I have two confusions here, could you help me figure out^^? my command line l...