Training AUGUSTUS

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training gene set and joingenes?

Last post by Kang « Thu Jun 27, 2019 1:06 pm

by Kang » Thu Jun 27, 2019 1:06 pm

0 Replies

50 Views

Last post by Kang
Thu Jun 27, 2019 1:06 pm
Could not get same result with example data

Last post by katharina « Sat Jun 23, 2018 4:39 pm
Replies: 1
by shunohki » Thu Jun 21, 2018 6:58 am

1 Replies

1529 Views

Last post by katharina
Sat Jun 23, 2018 4:39 pm
Species Not Available (Turtle)

Last post by katharina « Wed May 09, 2018 11:02 am
Replies: 1
by sam2010 » Tue May 08, 2018 9:17 pm

1 Replies

153 Views

Last post by katharina
Wed May 09, 2018 11:02 am
Training augustus with busco or?

Last post by katharina « Mon Apr 09, 2018 1:25 pm
Replies: 1
by Morko » Thu Mar 22, 2018 5:24 pm

1 Replies

211 Views

Last post by katharina
Mon Apr 09, 2018 1:25 pm
Training based on an existing profile

Last post by katharina « Mon Apr 09, 2018 1:12 pm
Replies: 1
by oliviam » Thu Mar 08, 2018 1:50 pm

1 Replies

237 Views

Last post by katharina
Mon Apr 09, 2018 1:12 pm
UTR training error?

Last post by katharina « Thu Nov 09, 2017 3:41 pm
Replies: 4
by xvazquezc » Tue Oct 03, 2017 11:52 am

4 Replies

438 Views

Last post by katharina
Thu Nov 09, 2017 3:41 pm
pre-compiled datasets

Last post by katharina « Tue Oct 24, 2017 12:53 pm
Replies: 2
by lucas.schmitz » Sun Aug 27, 2017 9:04 pm

2 Replies

319 Views

Last post by katharina
Tue Oct 24, 2017 12:53 pm
Error in etraining

Last post by katharina « Fri Mar 31, 2017 8:33 am
Replies: 1
by ckuanglim » Mon Mar 27, 2017 2:18 am

1 Replies

352 Views

Last post by katharina
Fri Mar 31, 2017 8:33 am
Error: Possibly "scipio" is not installed or not in your PATH

Last post by katharina « Fri Mar 31, 2017 8:29 am
Replies: 2
by eggland » Thu May 12, 2016 2:28 pm

2 Replies

851 Views

Last post by katharina
Fri Mar 31, 2017 8:29 am
GenBank format .gbff instead of .gb

Last post by katharina « Fri Mar 31, 2017 8:26 am
Replies: 1
by ferluz » Mon Aug 15, 2016 8:49 pm

1 Replies

604 Views

Last post by katharina
Fri Mar 31, 2017 8:26 am
Corrupt Genbank format error

Last post by katharina « Fri Mar 31, 2017 8:22 am
Replies: 1
by sansan » Tue Jul 12, 2016 1:25 pm

1 Replies

578 Views

Last post by katharina
Fri Mar 31, 2017 8:22 am
optimize_augustus.pl results in lower prediction accuracy??

Last post by katharina « Fri Mar 31, 2017 8:20 am
Replies: 1
by jonpalmer » Fri Jul 01, 2016 2:22 pm

1 Replies

682 Views

Last post by katharina
Fri Mar 31, 2017 8:20 am
Error when using filterBam on gsnap bam files

Last post by katharina « Fri Mar 31, 2017 8:17 am
Replies: 2
by PhilSchiffer » Mon Jun 27, 2016 3:20 pm

2 Replies

640 Views

Last post by katharina
Fri Mar 31, 2017 8:17 am
One question about the using Scipio to do gene prediction

Last post by katharina « Mon Dec 14, 2015 11:47 am
Replies: 14
by Yafei » Mon Nov 30, 2015 11:54 am

14 Replies

2238 Views

Last post by katharina
Mon Dec 14, 2015 11:47 am
Some confusions about optimize_augustus.pl

Last post by Yafei « Mon Nov 30, 2015 11:55 am
Replies: 2
by Yafei » Mon Nov 30, 2015 2:51 am

2 Replies

753 Views

Last post by Yafei
Mon Nov 30, 2015 11:55 am
AutoAug.pl running with PASA+GMAP

Last post by katharina « Fri Nov 20, 2015 1:16 pm
Replies: 1
by katharina » Fri Nov 20, 2015 1:16 pm

1 Replies

617 Views

Last post by katharina
Fri Nov 20, 2015 1:16 pm
AutoAugustus starting PASA at pipline 21

Last post by katharina « Fri Nov 20, 2015 1:02 pm
Replies: 3
by katharina » Fri Nov 20, 2015 1:02 pm

3 Replies

747 Views

Last post by katharina
Fri Nov 20, 2015 1:02 pm
Problem etraining CEGMA input

Last post by katharina « Fri Nov 20, 2015 1:00 pm
Replies: 1
by katharina » Fri Nov 20, 2015 1:00 pm

1 Replies

794 Views

Last post by katharina
Fri Nov 20, 2015 1:00 pm
How to take data input from databases for training of beta vulgaris genome

Last post by katharina « Fri Nov 20, 2015 12:56 pm
Replies: 1
by katharina » Fri Nov 20, 2015 12:56 pm

1 Replies

542 Views

Last post by katharina
Fri Nov 20, 2015 12:56 pm
training dataset availabilty

Last post by katharina « Fri Nov 20, 2015 12:50 pm
Replies: 1
by katharina » Fri Nov 20, 2015 12:50 pm

1 Replies

596 Views

Last post by katharina
Fri Nov 20, 2015 12:50 pm
running optimize_AUGUSTUS.pl with multiple cpus on SGE

Last post by katharina « Fri Nov 20, 2015 12:25 pm
Replies: 3
by katharina » Fri Nov 20, 2015 12:25 pm

3 Replies

956 Views

Last post by katharina
Fri Nov 20, 2015 12:25 pm
Does etraining overwrite previous models or refine them ?

Last post by katharina « Fri Nov 20, 2015 12:22 pm
Replies: 1
by katharina » Fri Nov 20, 2015 12:21 pm

1 Replies

583 Views

Last post by katharina
Fri Nov 20, 2015 12:22 pm
Scheme of pipeline

Last post by katharina « Thu Nov 19, 2015 8:05 pm
Replies: 1
by katharina » Thu Nov 19, 2015 8:05 pm

1 Replies

871 Views

Last post by katharina
Thu Nov 19, 2015 8:05 pm
any crude diagnostic for optimize_augustus.pl run progress?

Last post by katharina « Thu Nov 19, 2015 8:03 pm
Replies: 1
by katharina » Thu Nov 19, 2015 8:03 pm

1 Replies

567 Views

Last post by katharina
Thu Nov 19, 2015 8:03 pm
Problem converting trainingSetComplete.gff to trainingSetComplete.gb in autoAug.pl

Last post by katharina « Thu Nov 19, 2015 8:02 pm
Replies: 3
by katharina » Thu Nov 19, 2015 8:02 pm

3 Replies

671 Views

Last post by katharina
Thu Nov 19, 2015 8:02 pm
confused by the protocol of AUGUSTUS

Last post by katharina « Thu Nov 19, 2015 8:01 pm
Replies: 10
by katharina » Thu Nov 19, 2015 7:59 pm

10 Replies

1615 Views

Last post by katharina
Thu Nov 19, 2015 8:01 pm
Transcript sensitivity/specificity question

Last post by katharina « Thu Nov 19, 2015 7:54 pm
Replies: 1
by katharina » Thu Nov 19, 2015 7:54 pm

1 Replies

509 Views

Last post by katharina
Thu Nov 19, 2015 7:54 pm
running autoAug.pl on several CPUs

Last post by katharina « Thu Nov 19, 2015 7:44 pm
Replies: 1
by katharina » Thu Nov 19, 2015 7:44 pm

1 Replies

465 Views

Last post by katharina
Thu Nov 19, 2015 7:44 pm
High nucleotide sensitivity/specificity, zero gene level

Last post by katharina « Thu Nov 19, 2015 7:43 pm
Replies: 1
by katharina » Thu Nov 19, 2015 7:43 pm

1 Replies

517 Views

Last post by katharina
Thu Nov 19, 2015 7:43 pm
Train Augustus from RNA-Seq and genome alone

Last post by katharina « Thu Nov 19, 2015 7:36 pm
Replies: 4
by katharina » Thu Nov 19, 2015 7:35 pm

4 Replies

906 Views

Last post by katharina
Thu Nov 19, 2015 7:36 pm
Could not read the accuracy values out of predictions.txt

Last post by katharina « Thu Nov 19, 2015 7:32 pm
Replies: 2
by katharina » Thu Nov 19, 2015 7:31 pm

2 Replies

739 Views

Last post by katharina
Thu Nov 19, 2015 7:32 pm
AutoAug.pl "No such file or directory"

Last post by katharina « Thu Nov 19, 2015 6:48 pm
Replies: 6
by katharina » Thu Nov 19, 2015 6:46 pm

6 Replies

842 Views

Last post by katharina
Thu Nov 19, 2015 6:48 pm
Error with running autoAug.pl

Last post by katharina « Thu Nov 19, 2015 5:25 pm
Replies: 10
by katharina » Thu Nov 19, 2015 5:23 pm

10 Replies

1047 Views

Last post by katharina
Thu Nov 19, 2015 5:25 pm
augustus utr training error

Last post by katharina « Thu Nov 19, 2015 5:22 pm
Replies: 1
by katharina » Thu Nov 19, 2015 5:22 pm

1 Replies

444 Views

Last post by katharina
Thu Nov 19, 2015 5:22 pm
Specificity of augustus

Last post by katharina « Thu Nov 19, 2015 5:18 pm
Replies: 1
by katharina » Thu Nov 19, 2015 5:18 pm

1 Replies

533 Views

Last post by katharina
Thu Nov 19, 2015 5:18 pm
autoAug.pl error

Last post by katharina « Thu Nov 19, 2015 5:17 pm
Replies: 7
by katharina » Thu Nov 19, 2015 5:16 pm

7 Replies

904 Views

Last post by katharina
Thu Nov 19, 2015 5:17 pm
Problem with optimize_augustus.pl

Last post by katharina « Thu Nov 19, 2015 5:06 pm
Replies: 1
by katharina » Thu Nov 19, 2015 5:06 pm

1 Replies

444 Views

Last post by katharina
Thu Nov 19, 2015 5:06 pm
Comment on low gene level accuracy

Last post by katharina « Thu Nov 19, 2015 5:05 pm
Replies: 9
by katharina » Thu Nov 19, 2015 5:03 pm

9 Replies

1599 Views

Last post by katharina
Thu Nov 19, 2015 5:05 pm
Help with error while running etraining

Last post by katharina « Thu Nov 19, 2015 5:02 pm
Replies: 2
by katharina » Thu Nov 19, 2015 5:02 pm

2 Replies

520 Views

Last post by katharina
Thu Nov 19, 2015 5:02 pm
how to train AUGUSTUS for my study species with its own sequence and other species' protein

Last post by katharina « Thu Nov 19, 2015 5:00 pm
Replies: 5
by katharina » Thu Nov 19, 2015 4:58 pm

5 Replies

719 Views

Last post by katharina
Thu Nov 19, 2015 5:00 pm
Training with proteins - problems of ATG necessity

Last post by katharina « Thu Nov 19, 2015 3:45 pm
Replies: 1
by katharina » Thu Nov 19, 2015 3:45 pm

1 Replies

611 Views

Last post by katharina
Thu Nov 19, 2015 3:45 pm
Creating training set from assembled RNAseq transcripts

Last post by katharina « Thu Nov 19, 2015 3:43 pm
Replies: 4
by katharina » Thu Nov 19, 2015 3:43 pm

4 Replies

629 Views

Last post by katharina
Thu Nov 19, 2015 3:43 pm
runtime of optimize_augustus.pl

Last post by katharina « Thu Nov 19, 2015 3:26 pm
Replies: 1
by katharina » Thu Nov 19, 2015 3:26 pm

1 Replies

460 Views

Last post by katharina
Thu Nov 19, 2015 3:26 pm
buckets - curtrain - predictions

Last post by katharina « Thu Nov 19, 2015 3:23 pm
Replies: 1
by katharina » Thu Nov 19, 2015 3:23 pm

1 Replies

474 Views

Last post by katharina
Thu Nov 19, 2015 3:23 pm
autoAug.pl error when using with PASA

Last post by katharina « Thu Nov 19, 2015 3:21 pm
Replies: 1
by katharina » Thu Nov 19, 2015 3:21 pm

1 Replies

652 Views

Last post by katharina
Thu Nov 19, 2015 3:21 pm
Augustus on WGS and RNA-Seq data

Last post by katharina « Thu Nov 19, 2015 3:20 pm
Replies: 7
by katharina » Thu Nov 19, 2015 3:19 pm

7 Replies

934 Views

Last post by katharina
Thu Nov 19, 2015 3:20 pm
UTR annotation

Last post by katharina « Thu Nov 19, 2015 3:09 pm
Replies: 5
by katharina » Thu Nov 19, 2015 3:07 pm

5 Replies

986 Views

Last post by katharina
Thu Nov 19, 2015 3:09 pm
Augustus 3.0 etraining input format error

Last post by katharina « Thu Nov 19, 2015 3:02 pm
Replies: 3
by katharina » Thu Nov 19, 2015 3:02 pm

3 Replies

668 Views

Last post by katharina
Thu Nov 19, 2015 3:02 pm
improve existing AUGUSTUS parameters using RNA-Seq

Last post by katharina « Thu Nov 19, 2015 3:01 pm
Replies: 2
by katharina » Thu Nov 19, 2015 3:00 pm

2 Replies

530 Views

Last post by katharina
Thu Nov 19, 2015 3:01 pm
Error while running autoAug.pl

Last post by katharina « Thu Nov 19, 2015 2:50 pm
Replies: 6
by katharina » Thu Nov 19, 2015 2:47 pm

6 Replies

935 Views

Last post by katharina
Thu Nov 19, 2015 2:50 pm

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