ConesaLab SQANTI3 issues

ConesaLab / SQANTI3

Tool for the Quality Control of Long-Read Defined Transcriptomes

GNU General Public License v3.0

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issues

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[BUG] An error occurred while installing package bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1

#338 emsisson opened 9 hours ago
0
Bugfix: corrected the sign in difference to TTS/TSS

#337 Fabian-RY opened 13 hours ago
0
FIX: transcripts without known strands (with '.' strand) are redirected

#336 Fabian-RY opened 1 day ago
0
[BUG] Incomplete SQANTI3_filter output

#335 zhangkn3 opened 2 days ago
3
[BUG] IndexError: list index out of range

#334 YIGUIz opened 4 days ago
3
Fixes report failing when some some structural categories (mainly FSM, ISM, NIC or NNIC) were missing

#332 Fabian-RY closed 6 days ago
0
Modify write_collapsed_GFF_with_CDS in sqanti3_qc.py

#331 sbresnahan opened 1 week ago
0
Add NA replacement value for ratio_TSS column in ML Rescue

#330 aarzalluz closed 6 days ago
1
[BUG] IndexError: list index out of range

#329 yerry77 opened 1 week ago
4
Added compatibility for .gz compressed fasta/fastq isoforms to SQANTI3_QC

#326 Fabian-RY closed 2 weeks ago
0
Optionally ignore errors

#324 bschiffthaler closed 6 days ago
0
Dockerfile

#323 Fabian-RY closed 3 weeks ago
0
[BUG] sqanti3_filter.py is not filtering according to my custom rules

#322 dudududu12138 opened 4 weeks ago
1
Sqanti reads

#321 carolinamonzo closed 1 month ago
0
sqanti3_rescue - tags transcript_id, gene_id are absent from the attribute field [BUG]

#317 cathycoutu opened 2 months ago
1
Match `sqanti3_filter.py`'s no output prefix behavior in `sqanti3_rescue.py`

#316 skagawa2 opened 2 months ago
0
Missclassification of Genic Intron transcripts

#315 liniguez closed 2 months ago
1
[BUG] After running filter, the second column of the filtered gtf file is always `pacbio`, even if I'm using ONT data.

#314 dudududu12138 closed 2 months ago
2
[BUG]

#313 xiekunwhy closed 2 months ago
2
[FEATURE] support gzip'd input fastq files

#312 nick-youngblut closed 2 weeks ago
0
[BUG] pip install ultra-bioinformatics => Could not build wheels for edlib

#311 nick-youngblut closed 3 months ago
7
The installation of SQANTI3-5.2.1 encountered an error

#310 biochristmas closed 3 months ago
3
[BUG] Error running qc

#309 nkliutx closed 3 months ago
1
Issue generating rules filter report.

#304 tinatucci closed 3 months ago
2
Correction of the classfication of mono-exons

#303 alexpan00 closed 4 months ago
0
ML Filter output: Missing files, inverted ROC curve x-axis.

#301 klenhart closed 3 months ago
4
FileNotFoundError: Genome file "/chr_order.txt" does not exist

#300 francicco closed 4 months ago
2
FileNotFoundError: [Errno 2] No such file or directory: 'sqanti 3_output_splits/0/sqanti3_output_corrected.faa'

#298 lscdanson closed 4 months ago
18
Unique STAR run when running multiple chunks

#296 carolinamonzo closed 4 months ago
5
[BUG] squanti qc

#295 dawangran closed 4 months ago
6
GeneMark issue

#294 ghost closed 5 months ago
1
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

#291 TingQi2020 closed 5 months ago
3
sqanti_filter.py ML classifier variable importance table output error

#290 jelfman closed 5 months ago
9
How are fusions defined by SQANTI

#287 tky199996 closed 5 months ago
1
[BUG] list index out of range

#284 dawangran closed 5 months ago
1
Fixed a bug on classification of genic_intron (issue #255)

#283 alexpan00 closed 6 months ago
0
default rule filter also filtered out mono-exonic transcripts

#282 MengjunWu opened 6 months ago
0
SQANTI rules filtering with complex identifiers

#281 hyeon9 closed 5 months ago
2
Recover isoforms shorter than min_ref_len.

#280 lkondratova closed 6 months ago
0
Integrate Changes from Commit 2c9f581 for updating citation

#279 TianYuan-Liu closed 6 months ago
0
[BUG] fatal error in SQANTI3_report.R

#278 diekhans closed 6 months ago
3
Update SQANTI3 reference

#277 aarzalluz closed 6 months ago
0
Having output of examples check into git is problematic

#276 diekhans opened 6 months ago
0
Error with random forest when running ML rescue

#275 SamGallaher closed 5 months ago
2
BAM/SAM input option

#274 carolinamonzo opened 6 months ago
1
short_reads.py is. not robust

#272 diekhans closed 6 months ago
1
cDNA_Cupcake is painfuly to install, just get rid of it.

#271 diekhans closed 6 months ago
3
[BUG] errors in wiki Dependencies-and-installation.md

#270 diekhans closed 6 months ago
1
cdna_cupcake fusion_collate_info.py

#269 tky199996 closed 6 months ago
2
sqanti3_qc.py command not found

#268 Upendra19993 closed 6 months ago
1