EI-CoreBioinformatics mikado issues

EI-CoreBioinformatics / mikado

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.

https://mikado.readthedocs.io/en/stable/

GNU Lesser General Public License v3.0

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issues

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ValueError and Invalid Target End Point Errors during Mikado Serialization

#458 joseph144155 opened 1 month ago
0
serialise load BLAST data error (Cannot use a compiled regex as replacement pattern with regex=False)

#457 jolbi opened 3 months ago
3
Fix/gh workflows

#456 gemygk closed 3 months ago
0
Mikado pick does't add the CDS

#455 francicco opened 3 months ago
0
Bump scipy from 1.9.2 to 1.11.1

#454 dependabot[bot] closed 4 months ago
4
fix: pin mikado python dependencies

#453 gemygk closed 4 months ago
9
Assign transcripts to loci

#452 francicco opened 4 months ago
0
Error in mikado conda

#451 edugenetico opened 4 months ago
0
Error with mikado serialise: 'Engine' object has no attribute 'cursor'

#450 bbista opened 6 months ago
2
Error in rule asm_gff_stats

#449 jwli-code opened 8 months ago
0
can't install Mikado by different ways

#448 mezoderma opened 9 months ago
1
Parameters to avoid overlap

#447 xiekunwhy opened 11 months ago
0
Optimising Scoring file

#446 francicco closed 7 months ago
12
Unable to install mikado with mamba via multiple strategies

#445 isaacvock opened 1 year ago
4
scipy._build_utils is no longer available in scipy 1.10+

#444 boegel opened 1 year ago
0
fix: pip install mikado now works

#443 MmasterT closed 8 months ago
1
Error running serialise

#442 johannesnicolaus opened 1 year ago
1
Track gene/transcript ids

#441 francicco opened 1 year ago
0
bonus to the models, that are presented in several transcript assemblies

#440 sashulkaSh opened 1 year ago
0
Comparing two annotations

#439 AlexdeMendoza opened 1 year ago
1
error with running mikado

#438 ChemaMD closed 1 year ago
3
configuration error with mikado 2.3.2

#437 baozg opened 1 year ago
1
Designing specific scoring file

#436 allind opened 1 year ago
1
Best practice to use Mikado to score assembled lncRNA

#435 cc-prolix opened 1 year ago
3
Issue #433 - changing the order of operations in printing out the fil…

#434 lucventurini closed 1 year ago
3
Update requirements.txt

#433 ljyanesm closed 2 years ago
5
Mikado crashed, cause: unhashable type: 'list'

#432 dadrasarmin closed 2 years ago
2
Configuration.yaml is empty

#431 bbista closed 2 years ago
3
Mikado and PASA+EVM

#430 sanyalab closed 1 year ago
1
Mikado serialise sql3 error

#429 AlexdeMendoza closed 2 years ago
3
Is there a way to update all transcript to complete gene models?

#428 xiekunwhy closed 1 year ago
2
How to keep CDS information in input gtf files?

#427 xiekunwhy closed 2 years ago
6
Allow codon table to be set in mikado prepare

#426 swarbred closed 2 years ago
3
Merge bams or each bam separately?

#425 xiekunwhy closed 2 years ago
5
OSError: [Errno 27] File too large

#424 NJeanray closed 1 year ago
0
HSP uniqueness could fail in rare cases

#423 ljyanesm closed 2 years ago
1
sqlite3.IntegrityError during mikado serialise with blast homology

#422 JulienPPichon closed 2 years ago
21
Trinity doesn't give me any results

#421 NJeanray closed 2 years ago
3
Fix issue with empty blast results in tsv format

#420 ljyanesm closed 3 years ago
0
Solve performance issues affecting extra-dense superloci in ONT runs.

#419 lucventurini closed 3 years ago
1
Bulk add transcripts method

#418 lucventurini closed 3 years ago
1
[main_samview] fail to read the header from "-".

#417 NJeanray closed 2 years ago
4
Mikado using STAR : limitGenomeGenerateRAM

#416 NJeanray closed 3 years ago
4
mikdo pick throws this error and results in very few transcripts

#415 aseetharam closed 3 years ago
12
Using mikado to correct MAKER CDS sequences.

#414 keithforestdecker closed 3 years ago
2
Prepare bug with lowercase bases

#413 swarbred closed 3 years ago
0
Testing the installed module UnicodeDecodeError

#412 bismarck1008 closed 3 years ago
1
bug in transcriptchecker.py at line 255

#411 cooketho closed 3 years ago
3
Missing coding regions

#410 francicco closed 3 years ago
16
'list' object has no attribute 'finalize'

#409 francicco closed 3 years ago
2