ConesaLab/SQANTI3

Issues

• sqanti3_rescue.py: TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType

  #253 opened 10 months ago by ChiaraCaprioli
  35

• [BUG] SQANTI filter not producing output

  #342 opened 2 months ago by sparthib
  2

• [BUG] sqanti3_filter.py is not filtering according to my custom rules

  #322 opened 4 months ago by dudududu12138
  1

• sqanti3_rescue - tags transcript_id, gene_id are absent from the attribute field [BUG]

  #317 opened 5 months ago by cathycoutu
  1

• [BUG] Running SQANTI3_QC with chunks and no chunks produces differences in classification.txt

  #340 opened 3 months ago by Fabian-RY
  0

• [BUG] Incomplete SQANTI3_filter output

  #335 opened 3 months ago by zhangkn3
  5

• [BUG] IndexError: list index out of range

  #329 opened 3 months ago by yerry77
  4

• [BUG] IndexError: list index out of range

  #334 opened 3 months ago by YIGUIz
  3

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

  #338 opened 3 months ago by emsisson
  1

• [FEATURE] support gzip'd input fastq files

  #312 opened 3 months ago by nick-youngblut
  0

• Missclassification of Genic Intron transcripts

  #315 opened 5 months ago by liniguez
  1

• [BUG]

  #313 opened 5 months ago by xiekunwhy
  2

• [BUG] pip install ultra-bioinformatics => Could not build wheels for edlib

  #311 opened 6 months ago by nick-youngblut
  7

• [BUG] After running filter, the second column of the filtered gtf file is always `pacbio`, even if I'm using ONT data.

  #314 opened 5 months ago by dudududu12138
  2

• The isoform classification is not accurate for Genic Intron and Intergenic

  #255 opened 9 months ago by dolittle007
  18

• ML Filter output: Missing files, inverted ROC curve x-axis.

  #301 opened 6 months ago by klenhart
  4

• FileNotFoundError: [Errno 2] No such file or directory: 'sqanti 3_output_splits/0/sqanti3_output_corrected.faa'

  #298 opened 8 months ago by lscdanson
  18

• Issue generating rules filter report.

  #304 opened 6 months ago by tinatucci
  2

• The installation of SQANTI3-5.2.1 encountered an error

  #310 opened 6 months ago by biochristmas
  3

• [BUG] Error running qc

  #309 opened 6 months ago by nkliutx
  1

• [BUG] squanti qc

  #295 opened 7 months ago by dawangran
  6

• Errors in running sqanti3_filter.py

  #259 opened 10 months ago by Upendra19993
  6

• FileNotFoundError: Genome file "/chr_order.txt" does not exist

  #300 opened 7 months ago by francicco
  2

• Unique STAR run when running multiple chunks

  #296 opened 7 months ago by carolinamonzo
  5

• UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

  #291 opened 8 months ago by TingQi2020
  3

• [BUG] list index out of range

  #284 opened 8 months ago by dawangran
  1

• GeneMark issue

  #294 opened 8 months ago by guojunliu7
  1

• sqanti_filter.py ML classifier variable importance table output error

  #290 opened 8 months ago by jelfman
  9

• Difference in number of filtered isoforms in classification.txt and filtered isoform files

  #263 opened 8 months ago by Upendra19993
  3

• SQANTI rules filtering with complex identifiers

  #281 opened 8 months ago by hyeon9
  2

• How are fusions defined by SQANTI

  #287 opened 8 months ago by tky199996
  1

• illumna short reads

  #258 opened 10 months ago by tky199996
  2

• no report output when use --report both

  #266 opened 8 months ago by JXAUDZF
  7

• Error with random forest when running ML rescue

  #275 opened 8 months ago by SamGallaher
  2

• short_reads.py is. not robust

  #272 opened 9 months ago by diekhans
  1

• BAM/SAM input option

  #274 opened 9 months ago by carolinamonzo
  1

• default rule filter also filtered out mono-exonic transcripts

  #282 opened 9 months ago by MengjunWu
  0

• cDNA_Cupcake is painfuly to install, just get rid of it.

  #271 opened 9 months ago by diekhans
  3

• [BUG] fatal error in SQANTI3_report.R

  #278 opened 9 months ago by diekhans
  3

• cdna_cupcake fusion_collate_info.py

  #269 opened 9 months ago by tky199996
  2

• Having output of examples check into git is problematic

  #276 opened 9 months ago by diekhans
  0

• Getting error message when running sqanti3 quality control step

  #267 opened 9 months ago by Upendra19993
  1

• reads/isoforms to isoforms compatibility matrix

  #256 opened 10 months ago by houlinyu
  2

• Error generating Kallisto index

  #257 opened 10 months ago by Upendra19993
  3

• [BUG] errors in wiki Dependencies-and-installation.md

  #270 opened 9 months ago by diekhans
  1

• Regarding use of reference genome for SQANTI3

  #261 opened 10 months ago by Upendra19993
  1

• sqanti3_qc.py command not found

  #268 opened 9 months ago by Upendra19993
  1

• Issue running Squanti3 V 5.2- reading STAR jucntion/coverage file

  #260 opened 10 months ago by sentisci
  4

• Unexpected Number of Unique Genes in Report

  #252 opened 10 months ago by OEveSalar
  10

• Confusion about length and reference length column in SQANTI QC report

  #254 opened 10 months ago by TinyTasy
  1