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GenomeRIK
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tama
Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
GNU General Public License v3.0
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Update to Python 3
#87
jamestwebber
opened
1 year ago
1
Errors in TAMA GO: Formatting
#86
anchonggen
closed
1 year ago
3
IndexError: list index out of range tama_filter_primary_transcripts_orf.py
#85
bijendrabio
closed
1 year ago
5
IndexError: list index out of range
#84
DaveLutgen
closed
1 year ago
13
Error with duplicate trans id
#83
olechnwin
closed
1 year ago
3
converting main bed output to gtf
#82
olechnwin
closed
1 year ago
2
Error in TAMA merge
#81
anchonggen
closed
1 year ago
2
Error in tama_collapse: Genome seq is not the same length as query seq
#80
husensofteng
closed
1 year ago
8
Order of filter/post-processing steps?
#79
ejh243
closed
10 months ago
1
Error with exon end earlier than exon start
#78
skudashev
closed
2 years ago
7
Problem with exon ordering in tama_format_gtf_to_bed12_stringtie
#77
fairliereese
closed
2 years ago
2
Could tama_merge merge three files?
#76
zmz1988
closed
2 years ago
13
help needed in format converter
#75
zmz1988
closed
2 years ago
11
multiple UTR features in a gene
#74
hrrsjeong
closed
2 years ago
1
the tama bed output further analysis
#73
NahlaHu
closed
2 years ago
2
Can TAMA merge be used to combine a short read assembly and long read data without a reference genome?
#72
FarrahKhan1400
closed
2 years ago
4
IndexError: list index out of range
#71
mictadlo
opened
2 years ago
3
Find-Model-Changes pipeline
#70
mictadlo
closed
2 years ago
6
tama_merge only some chromosomes output to bed
#69
rob123king
closed
2 years ago
13
Preparing input files for TAMA
#68
mictadlo
closed
2 years ago
1
How do you avoid making very long introns?
#67
Trandamere
closed
2 years ago
0
Error reading merge.txt file when using tama_read_support_levels.py
#66
tzutongkao
closed
2 years ago
3
Can TAMA collapse deal with the pacbio transcripts without a reference genome?
#65
gouwei1
closed
2 years ago
1
Can TAMA create a bed12 file for just gene models represented gene_report.txt?
#64
noor-albader
closed
2 years ago
4
Running TAMA ORF + NMD prediction from non-TAMA output
#63
fairliereese
closed
2 years ago
7
Clarification splitting large SAM file to run collapse and then merge
#62
J-Calvelo
closed
2 years ago
7
CAGE-seq and Iso-seq integration
#61
Jung19911124
closed
2 years ago
2
tama_collapse.py different issue in sam and bam
#60
xiaonalu
closed
2 years ago
1
Tama collapse, Key error: X
#59
maysonlin
closed
3 years ago
3
Tama merge has so many genes
#58
Huangyizhong
closed
2 years ago
1
The difference between the TAMA and the collapse_isoforms_by_sam.py
#57
Huangyizhong
closed
3 years ago
1
tama_collapse error, line 6228, in <module>
#56
esterf
closed
2 years ago
10
TAMA merge - Minimum overlap ratio
#55
michaelway
closed
3 years ago
2
Tama Merge colour on UCSC Genome Browser
#54
SziKayLeung
closed
3 years ago
1
Repaired the bug of the judgement of 'Error with duplicate read ID in different sources'
#53
Ckenen
closed
2 years ago
1
tama_flnc_polya_cleanup.py fails for "A"-only sequences
#52
ebioman
closed
3 years ago
1
tama_cds_regions_bed_add issue
#51
emmabailey94
closed
3 years ago
1
tama_merge filelist error
#48
caiobrunharo
closed
3 years ago
1
Improve annotation
#47
cculma
closed
3 years ago
1
Hidden characters in shebang
#46
ebioman
closed
3 years ago
2
Can 'tama_flnc_polya_cleanup.py' input/output FASTQ or BAM format?
#45
frabanal
closed
3 years ago
3
Odd output from Tama Merge
#43
SziKayLeung
closed
3 years ago
7
tama_collapse error when writing variant file (IndexError: list index out of range)
#42
martsper
closed
3 years ago
14
log argument not work
#41
yichangyu
closed
3 years ago
3
BAM file is not supported for tama_collapse.py
#40
yichangyu
closed
3 years ago
2
ImportError: No module named pysam
#39
yichangyu
closed
3 years ago
1
KeyError: 73 mapped_flag = sam_flag_dict[sam_flag]
#37
kgit95
closed
3 years ago
10
Can I use FLAIR corrected alignment with tama collapse?
#36
HegedusB
closed
3 years ago
32
issues with tama_remove_fragment_models.py
#35
ariadnamorales
closed
3 years ago
3
tama_collapse.py --> retuning error: no groups found! [input sorted.bam from minimap2 using HQ polished reads from isoseq3]
#34
ariadnamorales
closed
3 years ago
11
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