ConesaLab/SQANTI3

Issues

• Isoforms are misplaced and contain deletions (in-house reference/annotation)

  #251 opened 9 months ago
  9

• ERROR: gtf "chr1" chromosome not found in genome reference file.

  #250 opened a year ago
  2

• ImportError: cannot import name 'mean' from 'scipy'

  #249 opened a year ago
  5

• corrected.genePred -genePredExt -allErrors -ignoreGroupsWithoutExons' returned non-zero exit status 255.

  #248 opened 10 months ago
  6

• GFFParser error with example data in sqanti_qc

  #247 opened a year ago
  2

• ployA tail

  #246 opened 10 months ago
  1

• Isoforms originating from exon and intron regions are annotated as intergenic

  #245 opened a year ago
  3

• The sign of diff_to_TSS and diff_to_TTS seem to be flipped

  #244 opened 2 months ago
  1

• Parallelization Error

  #243 opened 8 months ago
  4

• SQANTI3 QC fails when using sorted BAMs to calculate ratio TSS with splits enabled

  #242 opened a year ago
  2

• Corrected gtf and fasta file not created

  #241 opened 10 months ago
  4

• v5.2 reports version as 5.1.2

  #240 opened a year ago
  1

• Alternative tools for orf prediction

  #239 opened a year ago
  1

• R package 'RColorConesa' missing for sqanti3_filter.py in conda installation

  #238 opened a year ago
  1

• sqanti QC transcript_models_corrected.gtf

  #237 opened a year ago
  1

• Error in Pigeon Report Rscript.

  #236 opened 10 months ago
  2

• Strand assertion error in SQANTI3 QC

  #235 opened a year ago
  2

• r-rcolorconesa not found during v5.2 yml environment installation

  #234 opened a year ago
  3

• Alternative file for reference transcriptome annotation

  #233 opened a year ago
  2

• Question about gene_name/gene_id in gff3 file for tappAS

  #231 opened a year ago
  3

• CDS not annotated using isoAnnotLite

  #230 opened a year ago
  8

• pandas.errors.MergeError in ratio_TSS column when using many SR/BAM files as input

  #228 opened a year ago
  5

• Dockerfile for SQANTI3/5.1.2

  #227 opened 4 months ago
  9

• error with --short_reads

  #226 opened a year ago
  4

• IsoAnnotLite protein features are not transferred

  #225 opened 8 months ago
  2

• SQANTI3 QC throws GMST error during correctionPlusORF prediction

  #224 opened a year ago
  4

• ArrayMemoryError when calculating TSS ratio

  #223 opened a year ago
  1

• sqanti_qa report fails if there are no isoforms in a category

  #221 opened a year ago
  2

• version returned incorrect

  #220 opened a year ago
  2

• SQANTI3_report.pdf generation fails when one or more structural categories are empty

  #219 opened 3 months ago
  1

• Option to write TSV for each report table

  #218 opened a year ago
  2

• document install cdna_cupcake via bioconda

  #217 opened 10 months ago
  6

• understanding the dup isoforms in the classification file

  #216 opened a year ago
  2

• SQANTI3 not running with SR bam option

  #215 opened a year ago
  4

• OSError: [Errno 8] Exec format error: '/Users/sonyx/SQANTI3-5.1.2/utilities/gtfToGenePred'

  #214 opened a year ago
  4

• FLAIR vs TAMA collapse for Nanopore long read data

  #213 opened a year ago
  6

• sqanti hides import errors and makes it hard to debug

  #212 opened a year ago
  0

• "Transcript_id" and "gene_id" in sqanti_ccorrected.gtf

  #211 opened a year ago
  4

• IndexError: list index out of range

  #210 opened a year ago
  3

• Error with invalid IDs in SQANTI3 QC

  #209 opened a year ago
  2

• Error installing cDNA_Cupcake

  #208 opened 10 months ago
  18

• ERROR with using SR_bam

  #207 opened a year ago
  3

• mustOpen: Can't open ***/RNC_PR1_sqanti3_qc.genePred to write: No such file or directory

  #205 opened a year ago
  0

• pigeon report generating missing R scrips.

  #204 opened a year ago
  3

• Error Generating R Report when missing SC

  #202 opened 3 months ago
  7

• The _corrected.gtf.cds.gff is not generated when running SQANTI3 QC module

  #201 opened 2 months ago
  6

• how to generate pigeon reports from sqanti3_qc.py and qanti3_filter.py.

  #200 opened a year ago
  1

• SQANTI3 QC fail [Error on last system call, error code 256]

  #199 opened 2 years ago
  3

• fasta nomenclature vs fl_abundance PB nomenclature

  #198 opened 2 years ago
  0

• RTS_stage issue

  #197 opened 2 years ago
  0