BrooksLabUCSC flair issues

BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA

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issues

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Add FLAIR workflows to Dockstore

#385 diekhans opened 1 week ago
0
add documentation images sources and fix a help message

#384 diekhans closed 2 weeks ago
0
convert flair to a distributed application

#383 diekhans opened 2 weeks ago
0
flair collapse should be able to get reads from BAM as well as going back to FASTQ

#382 diekhans opened 2 weeks ago
0
flair correct guessing the format of junction input is confusing and brittle

#381 diekhans opened 2 weeks ago
0
flair-align --keep_supplementary is incorrectly named

#380 diekhans opened 3 weeks ago
0
exon start coordinate > end coordinate after collapse

#379 YIGUIz opened 1 month ago
0
FLAIR collapse fails after Minimap2 indexing without clear error

#378 lucilaviappiani opened 1 month ago
0
diffSplice - how it detects AS coordinates exon

#377 kwonej0617 opened 2 months ago
0
what's the meaning of *.unassigned.* files

#376 Taylorain opened 2 months ago
0
Issue with flair collapse subprocess subset_unassigned_reads.py

#375 mpizzagalli777 closed 1 month ago
2
Feature Request: `Flair collapse` does not support gzip compressed reference FASTAs

#374 maxgmarin opened 2 months ago
1
DRIMSeq cannot be triggered

#373 gocrag opened 2 months ago
1
flair correct - Reference sequence NC_037349.1 not found in annotations, skipping

#372 YIGUIz closed 2 months ago
2
FLAIR with noncanonical splice sites - collapse throws out reads due to bad alignment

#371 cafelton opened 2 months ago
1
too few isoforms

#370 YuLiu-PetersLab closed 2 months ago
1
Error in flair collapse

#369 Kristopher02 opened 2 months ago
0
switch from multiprocessing fork server to spawn server

#368 diekhans opened 3 months ago
0
flair collapse crashes on MacOS

#367 diekhans opened 3 months ago
0
updates to MaxOS ARM instructions

#366 diekhans closed 3 months ago
0
Flair collapse path issues on EasyBuild install.

#365 srbennett opened 3 months ago
3
conda install issues on Mac ARM systems

#364 diekhans opened 3 months ago
1
added documentattion on installing FLAIR on Apple ARM64 systems

#363 diekhans closed 3 months ago
0
regarding id with '-0' at the end of transcript id

#362 kwonej0617 opened 3 months ago
0
add --help to flair

#361 fizwit opened 3 months ago
0
flair --help throws runtime error

#360 fizwit opened 3 months ago
0
Flair collapse does not support .fa.gz

#359 vpeddu opened 3 months ago
0
Question on TSS/PAS support

#358 IceFreez3r opened 3 months ago
0
Failed at counting step for annotated isoform read support

#357 kyusikkimmn opened 3 months ago
0
Exon with negative length

#356 IceFreez3r opened 3 months ago
1
Extremely high cell barcode associations

#355 bayleaflet opened 4 months ago
0
plot_isoforms_usage duplication of isoforms in plot

#354 wdesaintjean closed 3 months ago
2
flair correct - FileNotFound %s_inconsistent.bed

#353 sguizard opened 4 months ago
1
failed test for flair correct

#352 zpliu1126 opened 4 months ago
0
Some question about FLAIR2 (doi: 10.1186/s13059-024-03301-y)

#351 bxZhang996 opened 4 months ago
0
Flair align & correct producing empty results & no error

#350 jrkirk61 opened 4 months ago
1
Running FLAIR with multiple samples

#349 lilif99 opened 4 months ago
0
flair collapse failing but error message isn't informative

#348 markram4 opened 4 months ago
0
No output from flair align after specifying --output

#347 kmcoyle opened 4 months ago
0
Set `--annotation_reliant` but still got novel single-exon genes

#346 dudududu12138 opened 4 months ago
0
Odd result after splitting bed by chromosomes

#345 dudududu12138 opened 4 months ago
0
Flair collapse runs so slow with big fastq file even though I split bed by chromosome

#344 dudududu12138 opened 4 months ago
0
How does flair quantification work?

#343 dudududu12138 opened 5 months ago
0
FLAIR plot_isoform_usage transcripts flipped

#342 lilif99 opened 5 months ago
1
Process termination at Step 5/5 in flair correct without error messages

#341 kataksk opened 5 months ago
1
FLAIR missing isoforms

#340 lilif99 opened 5 months ago
1
Collapse step didn't output a gtf file without a reference annotation

#339 dudududu12138 opened 6 months ago
0
ValueError in filter_isoforms_by_proportion_of_gene_expr.py

#338 byee4 opened 6 months ago
0
flair quantify problem error

#337 wdesaintjean closed 5 months ago
3
flair correct shows FileNotFoundError

#336 guo0814 opened 6 months ago
1