Predicting Genes with AUGUSTUS

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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

200 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

1878 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

661 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

670 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

834 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

1042 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

1234 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

846 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

755 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

845 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

1096 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

1039 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

1494 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

4010 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

1239 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

1354 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

1168 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

2740 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

1693 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

1657 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

4773 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

1177 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

1241 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

1316 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

1300 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

890 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

1438 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

859 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

1462 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

1177 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

1095 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

847 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

636 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

634 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

708 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

852 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

2917 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

672 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

707 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

1318 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

822 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

548 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

733 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

877 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

697 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

822 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

918 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

910 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

654 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

724 Views

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

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