AUGUSTUS Forum

by katharina on 21.06.2014 - 15:37 It depends on what you want to achieve. If you think that ESTs are more reliable than protein hints, then you should assign a higher priority to the ESTs, yes (that means a higher number). The hint priority determines which hint will be used in case of a contradic...

by Sam on 13.06.2014 - 06:57
hints priority
W.r.t my above question, can I just concatenate the two hints files and supply the file to Augustus or do I need to process them further? Thank you.

Originally posted in the old forum by Sam on 13.06.2014 - 06:39
Hi,
I have hints derived from ESTs and protein alignments. Looks like the default priority is 4 for both. Could you please tell me if I should be using higher priority for ESTs? Thank you.

by katharina on 04.07.2014 - 11:33 Yes, you are right, if you predict genes without a UTR model, CDS equal exons. In the output file, exons are in that case labeled as "initial", "internal", and "terminal". Example: scaffold36 AUGUSTUS gene 59 1324 0.13 + . g5 scaffold...

by ebioman on 04.07.2014 - 09:34 Solved Just to follow up. I think I understood the core of the problem. Essentially, if a model contains information about UTR regions (such as Arabidopsis), then Augustus is capable to predict exons and therefore this are subsequently annotated. If a UTR model is l...

by ebioman on 03.07.2014 - 16:32
Missed information
I forgot to add, that if I take an established plant model as Arabidopsis I receive with the same command exons (wrong annotated though).
The version I am using is 3.0.1

Originally posted in the old forum by ebioman on 03.07.2014 - 16:25 Hello I have a rather strange observation I trained Augustus for a new species and was rather successful in my opinion: 75% on the exon level and 45% at the gene level for both sensitivity and specificity. The strange thing though ...

by Vickie on 07.02.2013 - 11:00 Next error I ran into another error: grep complete ../pasa/trainingSetCandidates.fasta | perl -pe 's/>(\S+).*/$1\$/' 1> pasa.complete.lst grep: ../pasa/trainingSetCandidates.fasta: No such file or directory PASA has not constructed any complete training gene. Trainin...

by Vickie on 05.02.2013 - 15:06 I already found a solution. Simply commented lines 422-424 where autoAug.pl drops existing database. And as I can see, it works, DB exists, no errors from pasa. So I started pasa from pipeline index 14, because of different servers usage, it ran about 3 h and now is ...

by mario on 05.02.2013 - 14:11
I can't tell you. I suggest, in this case you run PASA by itself, locally. And then use the set of full length ORF gene structures as GFF training set in a run of autoAugTrain.

Originally posted in the old forum by Vickie on 31.01.2013 - 15:45 Hello! I have problem usin autoaug.pl with PASA. Exactly, because of some bug in PASA, I should skip the step 20 and start pasa at step 21. But I can't do it, 'cause starting autoaug.pl with changed line 426 ($perlCmdString="pe...

by katharina on 13.02.2014 - 10:29 The cegma pipeline must not necessarily generate gene structures that are regarded as "valid" by AUGUSTUS, and if an structure is invalid, it is skipped. It seems that in your case, not a single valid gene structure was produced. I sometimes get those er...

Originally posted in the old forum by ebioman on 12.02.2014 - 14:06 Hello I used the CEGMA output in order to train Augustus. 1. took the gff and converted it to Augustus style (did it with awk since I did not have your script 2. I used your script to extract genbank-format: ./gff2gbSmallDNA.pl ceg...

by katharina on 27.03.2013 - 12:25 I suggest you simply chop off everything in the read headers (the 1st, 5th, 9th, ... row that begins with an @) that occurs after the first space, and add a pairedness indicating ending. Before deciding on a suitable ending for entire file, I suggest you build you...

Originally posted in the old forum by mark on 26.03.2013 - 16:56 I have Illumina reads in _1.fastq and _2.fastq format, but they don't have /1 and /2 in the identifiers. And, note that I only have 1 row with identifiers (starting with @, those starting with + are removed, probably because its redun...

by katharina on 01.03.2013 - 15:22
Have you made it executable (e.g. using chmod)? Have you called it with its explicit path (if it was not added to your PATH variable), e.g. ./blat2hints.pl if it is located in the folder that you are currently working in?
Katharina

by Han on 28.02.2013 - 14:02
at the 3rd steps: Creates hints: I got this message: blat2hints.pl: command not found. any idea? I've copied the blat2hints.pl to my directory.

by Han on 26.02.2013 - 09:43
Thanks, I will try, hopefully it will work!

by EJ Blom on 26.02.2013 - 09:14
I think you should convert the cdna entries to a hint file.
A nice tutorial is here:
http://bioinf.uni-greifswald.de/bioinf/ ... porateESTs

Originally posted in the old forum by Han on 26.02.2013 - 06:28 Hi, I'm working on a primate genome, previously I run augustus for gene prediction and it's works well. Now I want to use augustus to do gene prediction and include the cdna file. I've download human cdna file form ensemble. Is this co...