BrooksLabUCSC flair issues

BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA

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flair correct - FileNotFound %s_inconsistent.bed

#353 sguizard opened 2 days ago
1
failed test for flair correct

#352 zpliu1126 opened 2 days ago
0
Some question about FLAIR2 (doi: 10.1186/s13059-024-03301-y)

#351 bxZhang996 opened 1 week ago
0
Flair align & correct producing empty results & no error

#350 jrkirk61 opened 1 week ago
1
Running FLAIR with multiple samples

#349 lilif99 opened 1 week ago
0
flair collapse failing but error message isn't informative

#348 markram4 opened 1 week ago
0
No output from flair align after specifying --output

#347 kmcoyle opened 2 weeks ago
0
Set `--annotation_reliant` but still got novel single-exon genes

#346 dudududu12138 opened 2 weeks ago
0
Odd result after splitting bed by chromosomes

#345 dudududu12138 opened 2 weeks ago
0
Flair collapse runs so slow with big fastq file even though I split bed by chromosome

#344 dudududu12138 opened 2 weeks ago
0
How does flair quantification work?

#343 dudududu12138 opened 3 weeks ago
0
FLAIR plot_isoform_usage transcripts flipped

#342 lilif99 opened 3 weeks ago
0
Process termination at Step 5/5 in flair correct without error messages

#341 kataksk opened 1 month ago
1
FLAIR missing isoforms

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

#339 dudududu12138 opened 1 month ago
0
ValueError in filter_isoforms_by_proportion_of_gene_expr.py

#338 byee4 opened 1 month ago
0
flair quantify problem error

#337 wdesaintjean closed 1 month ago
3
flair correct shows FileNotFoundError

#336 guo0814 opened 2 months ago
1
psl_to_sequence command

#335 sparthib opened 2 months ago
0
Hello, after splitting the BED file by chromosomes, we found that a single chromosome's BED file is 1.03G, which is larger than 1G. Can Flair Collapse currently handle a BED file of 1.03G?

#334 991031liurui opened 2 months ago
1
The naming of my isoforms is different from what is mentioned in your manual.

#333 gnilihzeux opened 2 months ago
0
How to concatenate bed files before flair collapse

#332 chenxing-zhang opened 3 months ago
2
allow flair correct to specify temporary directory

#331 diekhans opened 3 months ago
1
Incorrectly name flair align options is confusing

#330 diekhans opened 3 months ago
0
How to count the isoforms corresponding to each gene.

#329 anxuan-web closed 4 months ago
2
flair collapse--NameError: name 'blockcount' is not defined

#328 ChenOreo closed 4 months ago
4
Flair collapse issue

#327 TTT16 closed 4 months ago
13
add --split-prefix to collapse minimap command

#326 Jeltje opened 5 months ago
0
fix #180, thanks Colette

#325 Jeltje closed 5 months ago
0
error in flair quantify

#324 jakobht96 closed 4 months ago
9
Gene model naming issue

#323 sagnikbanerjee15 opened 5 months ago
1
Crash running flair collapse

#322 mbkodos opened 5 months ago
8
Set isoform abundance cutoff to FLAIR quantify

#321 ulbivin opened 5 months ago
1
A question about correct model

#320 anxuan-web opened 6 months ago
4
fixed #318; updated faq

#319 Jeltje closed 6 months ago
0
Flair quantify error message bug

#318 Chemical118 closed 6 months ago
1
ITD detection?

#316 itslittman opened 7 months ago
12
Not full length transcript

#315 yycc9897 closed 5 months ago
2
Running collapse_isoforms_precise.py in a main entry point

#314 andyjslee closed 6 months ago
2
merging code of conduct and discussion

#313 Jeltje closed 7 months ago
0
Flair collapse stuck at "renaming isoforms using gtf" without error

#311 dmanahan1 closed 5 months ago
3
diffSplice : No such file or directory: 'call_diffsplice_events.py'

#309 CorentinAube closed 5 months ago
1
Running Flair with multiple samples and replicates

#308 benpiticaru closed 5 months ago
1
diffSplice files are empty

#307 ghofrankothoum closed 5 months ago
1
FLAIR could improve alignments by passing minimap2 splice junctions

#306 diekhans opened 9 months ago
3
Unexpected entries in gtf file after flair collapse

#305 juanfraitu1 closed 8 months ago
1
Issues implementing FLAIR2

#304 Max-Tomlinson closed 6 months ago
1
Question regarding sequencing depth and collapse step

#303 wuy24 closed 6 months ago
1
Transcript read number

#302 seongwoohan closed 9 months ago
0
equal with base

#301 Jeltje closed 10 months ago
0