ablab IsoQuant issues - Githubissues

ablab / IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

https://ablab.github.io/IsoQuant/

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issues

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inconsistency between transcript_tpm.tsv and transcript_model_tpm.tsv

#248 Mangosteen24 opened 4 hours ago
0
input illumina bam

#247 JhinJhinJhin opened 2 days ago
0
Tweaking minimap2 parameters in Isoquant

#246 sanyalab opened 3 days ago
1
Issues in KeyError: 'novel'

#245 kerrwelton opened 4 days ago
4
Repeating error mesage: [W::hts_idx_load3] The index file is older than the data file:

#244 zli-lilly opened 6 days ago
10
Understanding how inconsistent reads are reused for de novo discovery

#243 omarelgarwany opened 1 week ago
3
Missing reference genes

#242 JC-therea closed 1 week ago
2
Visualize.py with linear output

#241 ljwharbers opened 1 week ago
1
GFF3 cannot be recognized

#240 sanyalab opened 1 week ago
4
Resolve multple non-informative assignmets

#239 andrewprzh closed 2 weeks ago
0
BrokenProcessPool Error when Running IsoQuant with Custom GTF

#238 lebronzhong opened 2 weeks ago
1
Reads duplicated in read_assignments, leading to multiple identical transcripts

#236 jamestwebber closed 4 days ago
5
isoquant log file

#235 KMbio43 closed 2 weeks ago
4
Single cell data one library with different conditions

#234 vasikara17 opened 3 weeks ago
2
Ambiguous Novel Transcript Locations and Merging Transcript Models

#233 BenneyMRArgue opened 3 weeks ago
2
I was able to run smoothly after setting the parameter 'ulimit -n 1000000', thanks!

#232 lmulroney opened 3 weeks ago
3
How to handling Transcripts without strand information in IsoQuant GTF File

#231 bxZhang996 opened 3 weeks ago
3
No CDS in the novel genes predicted by Isoquant

#230 sqwwww opened 1 month ago
1
Clarification on the definition of spanning for reads that terminate in the middle of an exon for `exclude_counts`

#229 skagawa2 closed 3 weeks ago
3
How to Process or Filter the Merged GTF File After Using Isoquant

#228 lebronzhong opened 1 month ago
3
added test for alignment_info.py

#227 cat-bug closed 1 month ago
0
How do I specify FLNC reads in IsoQuant

#226 sanyalab opened 1 month ago
4
Transcript quantification results are inconsistent

#225 biochristmas opened 1 month ago
3
Issue #222 - YAML support

#224 jackfreeman88 closed 1 month ago
4
Feature request: add command line option to specify desired output type

#223 ljwharbers closed 1 month ago
2
Visualize.py?

#222 ccmeth closed 1 month ago
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 JhinJhinJhin opened 1 month ago
7
Add visualizer

#220 andrewprzh closed 1 month ago
0
Failing with assertion error: "Gene and transcript records have unequal strands"...but they don't?

#219 jamestwebber closed 1 month ago
9
Dramatically speed up grouped counts for all features

#218 andrewprzh closed 1 month ago
0
TEST FAILED after installation of 3.4.2

#217 giuliafois closed 2 months ago
2
Remove similar transcripts before assigning reads

#216 andrewprzh closed 2 months ago
0
isoquant.py --test issue

#215 sophielemoine closed 2 months ago
3
Disk based mmr hybrid

#213 andrewprzh closed 2 months ago
0
Disk based mmr

#212 andrewprzh closed 2 months ago
1
multiple single cell samples

#211 wanghlv closed 4 days ago
5
Long time to run 80+ samples togather

#210 yuyun-zhang closed 1 month ago
3
Memory usage

#209 omarelgarwany closed 2 months ago
9
Choosing the ‘--data_type’ parameter for combined PacBio CCS and Nanopore data

#208 biochristmas closed 1 month ago
4
A Novel transcript without high-confidence reads support

#207 yuyun-zhang opened 3 months ago
2
invalid continuation byte error

#206 cariocow closed 4 days ago
7
Question about exon counting

#205 weib3 closed 1 month ago
3
read assignments file interpretation

#204 sparthib closed 1 month ago
6
Under the Reference-base model, TSS and TTS are not accurately annotated.

#203 zpliu1126 opened 3 months ago
3
trying to understand the `OUT.novel_vs_known.SQANTI-like.tsv`

#202 sparthib closed 1 month ago
5
added tests for serialization.py

#201 cat-bug closed 3 months ago
1
An inaccurate annotation

#200 zpliu1126 opened 3 months ago
3
if isoquant perfomed the isoform collapse?

#199 wjcre2023 closed 2 months ago
1
Pipeline - combine assembly and reads

#198 KristinaGagalova closed 2 months ago
1
Isoquant seems stuck

#197 francicco closed 1 month ago
16