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ConesaLab
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SQANTI3
Tool for the Quality Control of Long-Read Defined Transcriptomes
GNU General Public License v3.0
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Getting error message when running sqanti3 quality control step
#267
Upendra19993
closed
6 months ago
1
no report output when use --report both
#266
JXAUDZF
closed
5 months ago
7
Difference in number of filtered isoforms in classification.txt and filtered isoform files
#263
Upendra19993
closed
5 months ago
3
Issue template
#262
carolinamonzo
closed
7 months ago
0
Regarding use of reference genome for SQANTI3
#261
Upendra19993
closed
7 months ago
1
Issue running Squanti3 V 5.2- reading STAR jucntion/coverage file
#260
sentisci
closed
7 months ago
4
Errors in running sqanti3_filter.py
#259
Upendra19993
closed
7 months ago
6
illumna short reads
#258
tky199996
closed
7 months ago
2
Error generating Kallisto index
#257
Upendra19993
closed
7 months ago
3
reads/isoforms to isoforms compatibility matrix
#256
houlinyu
closed
7 months ago
2
The isoform classification is not accurate for Genic Intron and Intergenic
#255
dolittle007
closed
6 months ago
18
Confusion about length and reference length column in SQANTI QC report
#254
TinyTasy
closed
7 months ago
1
sqanti3_rescue.py: TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType
#253
ChiaraCaprioli
closed
7 months ago
11
Unexpected Number of Unique Genes in Report
#252
OEveSalar
closed
7 months ago
10
Isoforms are misplaced and contain deletions (in-house reference/annotation)
#251
eprdz
closed
6 months ago
9
ERROR: gtf "chr1" chromosome not found in genome reference file.
#250
mianlee
closed
8 months ago
2
ImportError: cannot import name 'mean' from 'scipy'
#249
mianlee
closed
8 months ago
5
corrected.genePred -genePredExt -allErrors -ignoreGroupsWithoutExons' returned non-zero exit status 255.
#248
Xingliang888
closed
7 months ago
5
GFFParser error with example data in sqanti_qc
#247
chaesee1
closed
8 months ago
2
ployA tail
#246
dawangran
closed
7 months ago
1
Isoforms originating from exon and intron regions are annotated as intergenic
#245
ZhangHaibo-777
closed
8 months ago
3
The sign of diff_to_TSS and diff_to_TTS seem to be flipped
#244
ryanpe13002
opened
9 months ago
1
Parallelization Error
#243
eprdz
closed
5 months ago
4
SQANTI3 QC fails when using sorted BAMs to calculate ratio TSS with splits enabled
#242
ryanpe13002
closed
8 months ago
2
Corrected gtf and fasta file not created
#241
jchariker
closed
7 months ago
4
v5.2 reports version as 5.1.2
#240
mkostich
closed
10 months ago
1
Alternative tools for orf prediction
#239
kdm9
opened
11 months ago
1
R package 'RColorConesa' missing for sqanti3_filter.py in conda installation
#238
jowodo
closed
10 months ago
1
sqanti QC transcript_models_corrected.gtf
#237
dawangran
closed
10 months ago
1
Error in Pigeon Report Rscript.
#236
unique379r
closed
7 months ago
2
Strand assertion error in SQANTI3 QC
#235
dawangran
closed
10 months ago
2
r-rcolorconesa not found during v5.2 yml environment installation
#234
stambolliualen
closed
12 months ago
3
Alternative file for reference transcriptome annotation
#233
Jung19911124
closed
10 months ago
2
Updates from SQANTI3 paper review
#232
aarzalluz
closed
1 year ago
0
Question about gene_name/gene_id in gff3 file for tappAS
#231
nadjano
closed
12 months ago
3
CDS not annotated using isoAnnotLite
#230
Ajay-097
opened
1 year ago
8
problem when using +4 SR files solved
#229
almart7
closed
1 year ago
0
pandas.errors.MergeError in ratio_TSS column when using many SR/BAM files as input
#228
ESWRKJ
closed
1 year ago
5
Dockerfile for SQANTI3/5.1.2
#227
skchronicles
closed
3 weeks ago
9
error with --short_reads
#226
ESWRKJ
closed
1 year ago
4
IsoAnnotLite protein features are not transferred
#225
mintstella0419
closed
5 months ago
2
SQANTI3 QC throws GMST error during correctionPlusORF prediction
#224
ESWRKJ
closed
1 year ago
4
ArrayMemoryError when calculating TSS ratio
#223
skudashev
closed
1 year ago
1
work around ggploty errors when a structural category has no isoforms
#222
diekhans
closed
1 year ago
0
sqanti_qa report fails if there are no isoforms in a category
#221
diekhans
closed
1 year ago
2
version returned incorrect
#220
mkostich
closed
1 year ago
2
SQANTI3_report.pdf generation fails when one or more structural categories are empty
#219
mkostich
closed
6 days ago
1
Option to write TSV for each report table
#218
diekhans
opened
1 year ago
2
document install cdna_cupcake via bioconda
#217
diekhans
closed
7 months ago
6
understanding the dup isoforms in the classification file
#216
alexyfyf
opened
1 year ago
2
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