Predicting Genes with AUGUSTUS

Moderator: bioinf

New Topic

71 topics

Topics

Replies

Views

Last post

transfer reference gene names to predicted sequences

Last post by anhanijr « Wed Oct 02, 2019 4:06 pm

by anhanijr » Wed Oct 02, 2019 4:06 pm

0 Replies

76 Views

Last post by anhanijr
Wed Oct 02, 2019 4:06 pm
Recompiling Augustus for short introns

Last post by kbseah « Wed May 08, 2019 5:48 pm

by kbseah » Wed May 08, 2019 5:48 pm

0 Replies

1803 Views

Last post by kbseah
Wed May 08, 2019 5:48 pm
meaning of attribues in GFF output

Last post by ddrddr « Sat Apr 20, 2019 1:03 am

by ddrddr » Sat Apr 20, 2019 1:03 am

0 Replies

580 Views

Last post by ddrddr
Sat Apr 20, 2019 1:03 am
executing augustus

Last post by samou1992 « Thu Apr 11, 2019 4:30 am

by samou1992 » Thu Apr 11, 2019 4:30 am

0 Replies

568 Views

Last post by samou1992
Thu Apr 11, 2019 4:30 am
AUGUSTUS 3.3 hanging on contig

Last post by PKooij « Thu Apr 12, 2018 4:50 pm
Replies: 2
by PKooij » Tue Apr 10, 2018 11:01 am

2 Replies

707 Views

Last post by PKooij
Thu Apr 12, 2018 4:50 pm
augustus - aborted (core dumped)

Last post by katharina « Mon Jan 29, 2018 9:12 am
Replies: 1
by psb21 » Fri Dec 09, 2016 11:39 am

1 Replies

940 Views

Last post by katharina
Mon Jan 29, 2018 9:12 am
Augustus PPX: Invalid block no. in SubstateModel::blockNoOfB

Last post by katharina « Mon Jan 29, 2018 9:08 am
Replies: 2
by lkremer » Wed Apr 13, 2016 4:30 pm

2 Replies

1120 Views

Last post by katharina
Mon Jan 29, 2018 9:08 am
bam2hints created an empty gff file

Last post by katharina « Mon Jan 29, 2018 9:07 am
Replies: 1
by Jung » Mon May 08, 2017 4:35 am

1 Replies

736 Views

Last post by katharina
Mon Jan 29, 2018 9:07 am
Augustus 3.3 stuck run

Last post by katharina « Mon Jan 29, 2018 9:07 am
Replies: 1
by matsepp » Tue Dec 19, 2017 3:15 pm

1 Replies

652 Views

Last post by katharina
Mon Jan 29, 2018 9:07 am
protein hints - required scripts

Last post by katharina « Fri Mar 31, 2017 8:39 am
Replies: 1
by psb21 » Thu Dec 01, 2016 2:49 am

1 Replies

768 Views

Last post by katharina
Fri Mar 31, 2017 8:39 am
filterBAM error

Last post by katharina « Fri Mar 31, 2017 8:38 am
Replies: 1
by francicco » Mon Jun 20, 2016 8:15 pm

1 Replies

1010 Views

Last post by katharina
Fri Mar 31, 2017 8:38 am
Parallel Comparative Genome Prediction?

Last post by sujaikumar « Thu May 26, 2016 10:52 am
Replies: 3
by katharina » Thu Nov 19, 2015 5:26 pm

3 Replies

933 Views

Last post by sujaikumar
Thu May 26, 2016 10:52 am
Extracting genes from newly sequenced data

Last post by katharina « Mon Apr 18, 2016 9:26 am
Replies: 3
by Bharat » Fri Mar 11, 2016 3:30 am

3 Replies

1372 Views

Last post by katharina
Mon Apr 18, 2016 9:26 am
extract gene sequence from AUGUSTUS predictions

Last post by lingonghua « Tue Dec 01, 2015 3:27 am
Replies: 10
by katharina » Fri Nov 20, 2015 1:28 pm

10 Replies

3704 Views

Last post by lingonghua
Tue Dec 01, 2015 3:27 am
How to cite

Last post by katharina « Fri Nov 20, 2015 1:30 pm
Replies: 1
by katharina » Fri Nov 20, 2015 1:30 pm

1 Replies

1160 Views

Last post by katharina
Fri Nov 20, 2015 1:30 pm
non-canonical splice site patterns

Last post by katharina « Fri Nov 20, 2015 1:25 pm
Replies: 1
by katharina » Fri Nov 20, 2015 1:25 pm

1 Replies

1271 Views

Last post by katharina
Fri Nov 20, 2015 1:25 pm
extrinstic.cfg

Last post by katharina « Fri Nov 20, 2015 1:24 pm
Replies: 1
by katharina » Fri Nov 20, 2015 1:24 pm

1 Replies

1080 Views

Last post by katharina
Fri Nov 20, 2015 1:24 pm
filterBam execution time

Last post by katharina « Fri Nov 20, 2015 1:22 pm
Replies: 7
by katharina » Fri Nov 20, 2015 1:21 pm

7 Replies

2498 Views

Last post by katharina
Fri Nov 20, 2015 1:22 pm
bamtools filter

Last post by katharina « Fri Nov 20, 2015 1:21 pm
Replies: 3
by katharina » Fri Nov 20, 2015 1:20 pm

3 Replies

1570 Views

Last post by katharina
Fri Nov 20, 2015 1:21 pm
filterBam and tophat2 question

Last post by katharina « Fri Nov 20, 2015 1:18 pm
Replies: 3
by katharina » Fri Nov 20, 2015 1:17 pm

3 Replies

1530 Views

Last post by katharina
Fri Nov 20, 2015 1:18 pm
AUGUSTUS for transcriptome

Last post by katharina « Fri Nov 20, 2015 1:14 pm
Replies: 15
by katharina » Fri Nov 20, 2015 1:09 pm

15 Replies

4258 Views

Last post by katharina
Fri Nov 20, 2015 1:14 pm
Branch sites in introns (and other conserved regions) used for gene prediction

Last post by katharina « Fri Nov 20, 2015 1:08 pm
Replies: 1
by katharina » Fri Nov 20, 2015 1:08 pm

1 Replies

1096 Views

Last post by katharina
Fri Nov 20, 2015 1:08 pm
augustus command for EVM

Last post by katharina « Fri Nov 20, 2015 1:07 pm
Replies: 1
by katharina » Fri Nov 20, 2015 1:07 pm

1 Replies

1152 Views

Last post by katharina
Fri Nov 20, 2015 1:07 pm
hints priority

Last post by katharina « Fri Nov 20, 2015 1:07 pm
Replies: 2
by katharina » Fri Nov 20, 2015 1:06 pm

2 Replies

1223 Views

Last post by katharina
Fri Nov 20, 2015 1:07 pm
Augustus excludes exons

Last post by katharina « Fri Nov 20, 2015 1:04 pm
Replies: 3
by katharina » Fri Nov 20, 2015 1:04 pm

3 Replies

1188 Views

Last post by katharina
Fri Nov 20, 2015 1:04 pm
how to correctly use RNA-seq data

Last post by katharina « Fri Nov 20, 2015 12:59 pm
Replies: 1
by katharina » Fri Nov 20, 2015 12:59 pm

1 Replies

802 Views

Last post by katharina
Fri Nov 20, 2015 12:59 pm
How to include cdna file

Last post by katharina « Fri Nov 20, 2015 12:57 pm
Replies: 4
by katharina » Fri Nov 20, 2015 12:57 pm

4 Replies

1292 Views

Last post by katharina
Fri Nov 20, 2015 12:57 pm
bam2hints error in gsnap pipeline

Last post by katharina « Fri Nov 20, 2015 12:55 pm
Replies: 1
by katharina » Fri Nov 20, 2015 12:55 pm

1 Replies

782 Views

Last post by katharina
Fri Nov 20, 2015 12:55 pm
Estimation of prediction accuracy

Last post by katharina « Fri Nov 20, 2015 12:53 pm
Replies: 3
by katharina » Fri Nov 20, 2015 12:53 pm

3 Replies

1351 Views

Last post by katharina
Fri Nov 20, 2015 12:53 pm
Augustus prediction with RNASeq Hints

Last post by katharina « Fri Nov 20, 2015 12:52 pm
Replies: 3
by katharina » Fri Nov 20, 2015 12:51 pm

3 Replies

1060 Views

Last post by katharina
Fri Nov 20, 2015 12:52 pm
Reducing average length of gene structure predictions

Last post by katharina « Fri Nov 20, 2015 12:20 pm

by katharina » Fri Nov 20, 2015 12:20 pm

0 Replies

1009 Views

Last post by katharina
Fri Nov 20, 2015 12:20 pm
wrongly predicted protein fusions

Last post by katharina « Thu Nov 19, 2015 7:57 pm
Replies: 3
by katharina » Thu Nov 19, 2015 7:56 pm

3 Replies

741 Views

Last post by katharina
Thu Nov 19, 2015 7:57 pm
augustus hints and "No feasible path found in HMM" error message

Last post by katharina « Thu Nov 19, 2015 7:55 pm
Replies: 1
by katharina » Thu Nov 19, 2015 7:55 pm

1 Replies

566 Views

Last post by katharina
Thu Nov 19, 2015 7:55 pm
FeatureCollection::esource: invalid source key: P

Last post by katharina « Thu Nov 19, 2015 7:53 pm
Replies: 1
by katharina » Thu Nov 19, 2015 7:53 pm

1 Replies

558 Views

Last post by katharina
Thu Nov 19, 2015 7:53 pm
question on exonpart hints

Last post by katharina « Thu Nov 19, 2015 7:52 pm
Replies: 1
by katharina » Thu Nov 19, 2015 7:52 pm

1 Replies

638 Views

Last post by katharina
Thu Nov 19, 2015 7:52 pm
runExonerate.pl?

Last post by katharina « Thu Nov 19, 2015 7:51 pm
Replies: 3
by katharina » Thu Nov 19, 2015 7:51 pm

3 Replies

746 Views

Last post by katharina
Thu Nov 19, 2015 7:51 pm
RNA-Seq based prediction

Last post by katharina « Thu Nov 19, 2015 7:50 pm
Replies: 22
by katharina » Thu Nov 19, 2015 7:46 pm
1

2
22 Replies

2504 Views

Last post by katharina
Thu Nov 19, 2015 7:50 pm
RNA-Seq coverage in intron

Last post by katharina « Thu Nov 19, 2015 7:45 pm
Replies: 1
by katharina » Thu Nov 19, 2015 7:44 pm

1 Replies

599 Views

Last post by katharina
Thu Nov 19, 2015 7:45 pm
scipio output as hints?

Last post by katharina « Thu Nov 19, 2015 7:41 pm
Replies: 2
by katharina » Thu Nov 19, 2015 7:41 pm

2 Replies

620 Views

Last post by katharina
Thu Nov 19, 2015 7:41 pm
Tutorial - RNAseq reads with TopHat

Last post by katharina « Thu Nov 19, 2015 7:40 pm
Replies: 7
by katharina » Thu Nov 19, 2015 7:38 pm

7 Replies

1126 Views

Last post by katharina
Thu Nov 19, 2015 7:40 pm
filterBAM seg faults with A LOT of memory

Last post by katharina « Thu Nov 19, 2015 7:34 pm
Replies: 2
by katharina » Thu Nov 19, 2015 7:33 pm

2 Replies

749 Views

Last post by katharina
Thu Nov 19, 2015 7:34 pm
Predict genes from metagenomic eukaryotic contigs

Last post by katharina « Thu Nov 19, 2015 7:30 pm
Replies: 1
by katharina » Thu Nov 19, 2015 7:30 pm

1 Replies

486 Views

Last post by katharina
Thu Nov 19, 2015 7:30 pm
Reusing hints files with different isolates

Last post by katharina « Thu Nov 19, 2015 7:29 pm
Replies: 2
by katharina » Thu Nov 19, 2015 7:28 pm

2 Replies

653 Views

Last post by katharina
Thu Nov 19, 2015 7:29 pm
Different Augustus output using the same command line.

Last post by katharina « Thu Nov 19, 2015 7:27 pm
Replies: 3
by katharina » Thu Nov 19, 2015 7:27 pm

3 Replies

781 Views

Last post by katharina
Thu Nov 19, 2015 7:27 pm
Reducing the number of introns

Last post by katharina « Thu Nov 19, 2015 5:30 pm
Replies: 2
by katharina » Thu Nov 19, 2015 5:29 pm

2 Replies

616 Views

Last post by katharina
Thu Nov 19, 2015 5:30 pm
run time with extrinsic data

Last post by katharina « Thu Nov 19, 2015 5:28 pm
Replies: 3
by katharina » Thu Nov 19, 2015 5:27 pm

3 Replies

703 Views

Last post by katharina
Thu Nov 19, 2015 5:28 pm
Using many tophat2 bam files

Last post by katharina « Thu Nov 19, 2015 5:15 pm
Replies: 5
by katharina » Thu Nov 19, 2015 5:14 pm

5 Replies

803 Views

Last post by katharina
Thu Nov 19, 2015 5:15 pm
hint groups never obeyed

Last post by katharina « Thu Nov 19, 2015 5:11 pm
Replies: 4
by katharina » Thu Nov 19, 2015 5:09 pm

4 Replies

802 Views

Last post by katharina
Thu Nov 19, 2015 5:11 pm
Problem with runs of Ns

Last post by katharina « Thu Nov 19, 2015 5:07 pm
Replies: 1
by katharina » Thu Nov 19, 2015 5:07 pm

1 Replies

592 Views

Last post by katharina
Thu Nov 19, 2015 5:07 pm
how long will it take to run AUGUSTUS for ab initio prediction

Last post by katharina « Thu Nov 19, 2015 5:01 pm
Replies: 3
by katharina » Thu Nov 19, 2015 5:00 pm

3 Replies

631 Views

Last post by katharina
Thu Nov 19, 2015 5:01 pm

New Topic

71 topics

Return to Board Index

Forum permissions

You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum