ablab/IsoQuant

Issues

• Understanding how inconsistent reads are reused for de novo discovery

  #243 opened 4 months ago by omarelgarwany
  4

• Is it necessary to de-redundant the resulting transcript model?

  #257 opened 2 months ago by wjcre2023
  7

• Inconsistency between gene_grouped_counts_linear.tsv and read_assignments.tsv.gz?

  #258 opened 2 months ago by qsonehara
  3

• inconsistency between transcript_tpm.tsv and transcript_model_tpm.tsv

  #248 opened 3 months ago by Mangosteen24
  7

• Some reads are not recorded in the OUT.read_assignments.tsv.gz

  #261 opened 2 months ago by creaturemoon
  2

• Feature request: add command line option to specify desired output type

  #223 opened 5 months ago by ljwharbers
  4

• Handling BAM files with polyA trimmed

  #256 opened 2 months ago by omarelgarwany
  1

• Reference-based and model-based TPMs are vastly different

  #249 opened 3 months ago by siyer-broad
  6

• bgzipped ref fasta take much longer time

  #260 opened 2 months ago by baozg
  1

• adding extra parameters for minimap2

  #259 opened 2 months ago by baozg
  1

• antisense classification for ONT direct RNAseq data

  #255 opened 2 months ago by baishengjun
  1

• How do I specify FLNC reads in IsoQuant

  #226 opened 5 months ago by sanyalab
  6

• Question on consensus transcript sequences created after processing FLNC via Isoquant

  #254 opened 3 months ago by sanyalab
  2

• Exon counts when there are genes on both strands

  #253 opened 3 months ago by skagawa2
  2

• how does isoquant deal with same cellular barcode across replicate files?

  #252 opened 3 months ago by sparthib
  1

• Inconsistent read assignment with bam file

  #250 opened 3 months ago by airichli
  2

• Specify cutoff for number of reads or number of samples.

  #251 opened 3 months ago by liuzhenyu-yyy
  1

• input illumina bam

  #247 opened 4 months ago by JhinJhinJhin
  1

• Tweaking minimap2 parameters in Isoquant

  #246 opened 4 months ago by sanyalab
  1

• Repeating error mesage: [W::hts_idx_load3] The index file is older than the data file:

  #244 opened 4 months ago by zli-lilly
  10

• Issues in KeyError: 'novel'

  #245 opened 4 months ago by kerrwelton
  4

• GFF3 cannot be recognized

  #240 opened 4 months ago by sanyalab
  4

• Reads duplicated in read_assignments, leading to multiple identical transcripts

  #236 opened 4 months ago by jamestwebber
  5

• multiple single cell samples

  #211 opened 4 months ago by wanghlv
  5

• invalid continuation byte error

  #206 opened 4 months ago by cariocow
  7

• Visualize.py with linear output

  #241 opened 4 months ago by ljwharbers
  1

• Missing reference genes

  #242 opened 4 months ago by JC-therea
  2

• Ambiguous Novel Transcript Locations and Merging Transcript Models

  #233 opened 4 months ago by BenneyMRArgue
  2

• isoquant log file

  #235 opened 4 months ago by KMbio43
  4

• BrokenProcessPool Error when Running IsoQuant with Custom GTF

  #238 opened 4 months ago by lebronzhong
  1

• Single cell data one library with different conditions

  #234 opened 4 months ago by vasikara17
  2

• Choosing the ‘--data_type’ parameter for combined PacBio CCS and Nanopore data

  #208 opened 5 months ago by biochristmas
  4

• Clarification on the definition of spanning for reads that terminate in the middle of an exon for `exclude_counts`

  #229 opened 4 months ago by skagawa2
  3

• read assignments file interpretation

  #204 opened 5 months ago by sparthib
  6

• I was able to run smoothly after setting the parameter 'ulimit -n 1000000', thanks!

  #232 opened 4 months ago by lmulroney
  3

• Transcript quantification results are inconsistent

  #225 opened 5 months ago by biochristmas
  3

• How to Process or Filter the Merged GTF File After Using Isoquant

  #228 opened 5 months ago by lebronzhong
  3

• How to handling Transcripts without strand information in IsoQuant GTF File

  #231 opened 4 months ago by bxZhang996
  3

• No CDS in the novel genes predicted by Isoquant

  #230 opened 4 months ago by sqwwww
  1

• trying to understand the `OUT.novel_vs_known.SQANTI-like.tsv`

  #202 opened 5 months ago by sparthib
  5

• Failing with assertion error: "Gene and transcript records have unequal strands"...but they don't?

  #219 opened 5 months ago by jamestwebber
  9

• Visualize.py?

  #222 opened 5 months ago by ccmeth
  12

• issuesTraceback (most recent call last): File "/lustre/home/jianghao/mambaforge/envs/isoquant/bin/isoquant.py", line 808, in <module> main(sys.argv[1:])

  #221 opened 5 months ago by JhinJhinJhin
  7

• Question about exon counting

  #205 opened 5 months ago by weib3
  3

• Long time to run 80+ samples togather

  #210 opened 5 months ago by yuyun-zhang
  3

• TEST FAILED after installation of 3.4.2

  #217 opened 5 months ago by giuliafois
  2

• Memory usage

  #209 opened 6 months ago by omarelgarwany
  9

• isoquant.py --test issue

  #215 opened 6 months ago by sophielemoine
  3

• A Novel transcript without high-confidence reads support

  #207 opened 7 months ago by yuyun-zhang
  2

• Under the Reference-base model, TSS and TTS are not accurately annotated.

  #203 opened 7 months ago by zpliu1126
  3