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ComparativeGenomicsToolkit
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Comparative-Annotation-Toolkit
Apache License 2.0
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Liftover gff3 files?
#270
elcortegano
closed
3 years ago
0
AugustusCGP issue
#269
ymxNancy
opened
3 years ago
0
install error
#268
zhangyuxin1012
opened
3 years ago
0
What to align RNA-seq to
#267
samkleeman1
opened
3 years ago
0
Install with docker
#266
zhangyuxin1012
opened
3 years ago
0
Protein alignments never utilized in pipeline b/c exonerate output is incompatible with `exonerate2hints.pl`
#265
nspope
opened
3 years ago
3
assembly hub error about maxSize to udcFileReadAll
#264
mglgnn
opened
3 years ago
0
Unable to create directory
#263
olekto
opened
3 years ago
0
Getting toil to work with SLURM
#262
JackyHess
opened
3 years ago
0
Enhancements
#261
mhaukness-ucsc
closed
1 year ago
3
KeyError in TranscriptFasta
#260
alxsimon
opened
3 years ago
2
Filtered transMap does not make it into final annotation
#259
mhaukness-ucsc
opened
3 years ago
0
incorrect indentification of frameshifts in T2T V1.
#258
diekhans
opened
3 years ago
2
self contained dockerfile tested on travis
#257
ifiddes
opened
3 years ago
0
CAT consensus_gene_set output
#256
francicco
opened
3 years ago
162
TransMap error
#255
francicco
opened
3 years ago
0
Fix build errors.
#254
ghost
closed
3 years ago
0
HPRC test cases
#253
diekhans
opened
3 years ago
2
add validation and fixer script for chrom disjoint genes
#252
ifiddes
closed
3 years ago
0
parallize transmap step
#251
diekhans
opened
3 years ago
0
gene id misnamed in bigGenePred
#250
diekhans
opened
3 years ago
0
Make assembly hub structure more useful for adding to large hubs
#249
diekhans
opened
3 years ago
0
assert interval.data not in ref_interval_map
#248
chatla01
opened
3 years ago
4
Update dockerfile
#247
elcortegano
closed
3 years ago
1
output GFF3 sometimes doesn't have "gene" feature type entries for a gene
#246
mhaukness-ucsc
opened
3 years ago
0
hub bigGenePred has labelSeparator misspelled
#245
diekhans
opened
3 years ago
0
AugustusCGP error
#244
francicco
opened
3 years ago
59
error while handling error in pipeline modules
#243
diekhans
opened
3 years ago
0
assembly hubs should hide snake tracks by default
#242
diekhans
opened
3 years ago
0
Produce GFF3 files that are valid for input to CAT
#241
mhaukness-ucsc
opened
3 years ago
0
improve parental gene assignment
#240
diekhans
opened
3 years ago
1
external reference are not assigned a biotype
#239
diekhans
opened
3 years ago
0
Requiring toil version 5.0
#238
mhaukness-ucsc
closed
3 years ago
2
pretty printing jsons
#237
mhaukness-ucsc
closed
3 years ago
0
correct join of tuple and list
#236
diekhans
closed
3 years ago
0
=>> PBS: job killed: ncpus exceeded limit
#235
francicco
closed
3 years ago
0
Validate config files
#234
mhaukness-ucsc
opened
3 years ago
0
CAT gff3 output format
#233
francicco
closed
3 years ago
2
Toil + Singularity
#232
fbemm
opened
3 years ago
1
FilterTransMap fails if given empty transMap files
#231
mhaukness-ucsc
opened
3 years ago
0
Hgm fails with a HgmDriverTask RuntimeError
#230
bulak
opened
3 years ago
6
fix splice test
#229
ifiddes
closed
3 years ago
0
how did this ever work
#228
ifiddes
closed
3 years ago
0
fix parasail
#227
ifiddes
closed
3 years ago
0
Ref clusters
#226
ifiddes
closed
3 years ago
0
create test cases with small genomes
#225
diekhans
opened
3 years ago
1
try a bug fix for issue 218
#224
ifiddes
closed
3 years ago
0
gene_name and gene_id for CAT input of CAT output
#223
ifiddes
closed
3 years ago
0
External references should be validated for referencing contigs that are in the FASTA files
#222
ifiddes
opened
3 years ago
0
Annotate the reference species [possible?] and orthology inference
#221
francicco
opened
3 years ago
6
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