BrooksLabUCSC/flair issues and pull requests

#363 - added documentattion on installing FLAIR on Apple ARM64 systems

Pull Request - State: closed - Opened by diekhans 6 months ago

#362 - regarding id with '-0' at the end of transcript id

Issue - State: open - Opened by kwonej0617 6 months ago

#361 - add --help to flair

Pull Request - State: open - Opened by fizwit 6 months ago

#360 - flair --help throws runtime error

Issue - State: open - Opened by fizwit 6 months ago

#359 - Flair collapse does not support .fa.gz

Issue - State: open - Opened by vpeddu 6 months ago

#358 - Question on TSS/PAS support

Issue - State: open - Opened by IceFreez3r 6 months ago

#357 - Failed at counting step for annotated isoform read support

Issue - State: open - Opened by kyusikkimmn 6 months ago

#356 - Exon with negative length

Issue - State: open - Opened by IceFreez3r 7 months ago

#355 - Extremely high cell barcode associations

Issue - State: open - Opened by bayleaflet 7 months ago

#354 - plot_isoforms_usage duplication of isoforms in plot

Issue - State: closed - Opened by wdesaintjean 7 months ago - 2 comments

#353 - flair correct - FileNotFound %s_inconsistent.bed

Issue - State: open - Opened by sguizard 7 months ago - 1 comment

#352 - failed test for flair correct

Issue - State: open - Opened by zpliu1126 7 months ago

#351 - Some question about FLAIR2 (doi: 10.1186/s13059-024-03301-y)

Issue - State: open - Opened by bxZhang996 7 months ago

#350 - Flair align & correct producing empty results & no error

Issue - State: open - Opened by jrkirk61 7 months ago - 1 comment

#349 - Running FLAIR with multiple samples

Issue - State: open - Opened by lilif99 7 months ago

#348 - flair collapse failing but error message isn't informative

Issue - State: open - Opened by markram4 7 months ago

#347 - No output from flair align after specifying --output

Issue - State: open - Opened by kmcoyle 7 months ago

#346 - Set `--annotation_reliant` but still got novel single-exon genes

Issue - State: open - Opened by dudududu12138 7 months ago

#345 - Odd result after splitting bed by chromosomes

Issue - State: open - Opened by dudududu12138 8 months ago

#344 - Flair collapse runs so slow with big fastq file even though I split bed by chromosome

Issue - State: open - Opened by dudududu12138 8 months ago

#343 - How does flair quantification work?

Issue - State: open - Opened by dudududu12138 8 months ago

#342 - FLAIR plot_isoform_usage transcripts flipped

Issue - State: open - Opened by lilif99 8 months ago - 1 comment

#341 - Process termination at Step 5/5 in flair correct without error messages

Issue - State: open - Opened by kataksk 8 months ago - 1 comment

#340 - FLAIR missing isoforms

Issue - State: open - Opened by lilif99 9 months ago - 1 comment

#339 - Collapse step didn't output a gtf file without a reference annotation

Issue - State: open - Opened by dudududu12138 9 months ago

#338 - ValueError in filter_isoforms_by_proportion_of_gene_expr.py

Issue - State: open - Opened by byee4 9 months ago

#337 - flair quantify problem error

Issue - State: closed - Opened by wdesaintjean 9 months ago - 3 comments

#336 - flair correct shows FileNotFoundError

Issue - State: open - Opened by guo0814 9 months ago - 1 comment

#335 - psl_to_sequence command

Issue - State: open - Opened by sparthib 9 months ago

#334 - 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?

Issue - State: open - Opened by 991031liurui 10 months ago - 1 comment

#333 - The naming of my isoforms is different from what is mentioned in your manual.

Issue - State: open - Opened by gnilihzeux 10 months ago

#332 - How to concatenate bed files before flair collapse

Issue - State: open - Opened by chenxing-zhang 10 months ago - 2 comments

#331 - allow flair correct to specify temporary directory

Issue - State: open - Opened by diekhans 10 months ago - 1 comment

#330 - Incorrectly name flair align options is confusing

Issue - State: open - Opened by diekhans 10 months ago

#329 - How to count the isoforms corresponding to each gene.

Issue - State: closed - Opened by anxuan-web 12 months ago - 2 comments

#328 - flair collapse--NameError: name 'blockcount' is not defined

Issue - State: closed - Opened by ChenOreo 12 months ago - 4 comments

#327 - Flair collapse issue

Issue - State: closed - Opened by TTT16 about 1 year ago - 13 comments

#326 - add --split-prefix to collapse minimap command

Issue - State: open - Opened by Jeltje about 1 year ago

#325 - fix #180, thanks Colette

Pull Request - State: closed - Opened by Jeltje about 1 year ago

#324 - error in flair quantify

Issue - State: closed - Opened by jakobht96 about 1 year ago - 9 comments

#323 - Gene model naming issue

Issue - State: open - Opened by sagnikbanerjee15 about 1 year ago - 1 comment

#322 - Crash running flair collapse

Issue - State: open - Opened by mbkodos about 1 year ago - 8 comments

#321 - Set isoform abundance cutoff to FLAIR quantify

Issue - State: open - Opened by ulbivin about 1 year ago - 1 comment

#320 - A question about correct model

Issue - State: open - Opened by anxuan-web about 1 year ago - 4 comments

#319 - fixed #318; updated faq

Pull Request - State: closed - Opened by Jeltje about 1 year ago

#318 - Flair quantify error message bug

Issue - State: closed - Opened by Chemical118 about 1 year ago - 1 comment

#316 - ITD detection?

Issue - State: open - Opened by itslittman about 1 year ago - 12 comments

#315 - Not full length transcript

Issue - State: closed - Opened by yycc9897 about 1 year ago - 2 comments

#314 - Running collapse_isoforms_precise.py in a main entry point

Issue - State: closed - Opened by andyjslee about 1 year ago - 2 comments

#313 - merging code of conduct and discussion

Pull Request - State: closed - Opened by Jeltje about 1 year ago

#311 - Flair collapse stuck at "renaming isoforms using gtf" without error

Issue - State: closed - Opened by dmanahan1 about 1 year ago - 3 comments

#309 - diffSplice : No such file or directory: 'call_diffsplice_events.py'

Issue - State: closed - Opened by CorentinAube over 1 year ago - 1 comment

#308 - Running Flair with multiple samples and replicates

Issue - State: closed - Opened by benpiticaru over 1 year ago - 1 comment

#307 - diffSplice files are empty

Issue - State: closed - Opened by ghofrankothoum over 1 year ago - 1 comment

#306 - FLAIR could improve alignments by passing minimap2 splice junctions

Issue - State: open - Opened by diekhans over 1 year ago - 3 comments
Labels: enhancement

#305 - Unexpected entries in gtf file after flair collapse

Issue - State: closed - Opened by juanfraitu1 over 1 year ago - 1 comment

#304 - Issues implementing FLAIR2

Issue - State: closed - Opened by Max-Tomlinson over 1 year ago - 1 comment
Labels: Old ticket; not enough info to proceed.

#303 - Question regarding sequencing depth and collapse step

Issue - State: closed - Opened by wuy24 over 1 year ago - 1 comment

#302 - Transcript read number

Issue - State: closed - Opened by seongwoohan over 1 year ago

#301 - equal with base

Pull Request - State: closed - Opened by Jeltje over 1 year ago

#300 - Refactor

Pull Request - State: closed - Opened by Jeltje over 1 year ago

#299 - Translate predictProductivity output to protein

Issue - State: closed - Opened by andreas-wilm over 1 year ago - 4 comments

#298 - Make FLAIR source & packaging structure not weird

Issue - State: open - Opened by diekhans over 1 year ago
Labels: enhancement

#297 - readthedocs change

Pull Request - State: closed - Opened by Jeltje over 1 year ago

#296 - MarkD updates for py3.11 and some code cleanup

Pull Request - State: closed - Opened by Jeltje over 1 year ago

#295 - work around for python 3.11 and a few other things

Pull Request - State: closed - Opened by diekhans over 1 year ago

#294 - Improve documentation of algorithm is readthedocs

Issue - State: open - Opened by diekhans over 1 year ago
Labels: AddToManual

#293 - flair correct doesn't exit non-zero when an invalid argument is supplied

Issue - State: open - Opened by diekhans over 1 year ago - 3 comments

#292 - Refactor branch with fixes for #290 and #291

Pull Request - State: closed - Opened by Jeltje over 1 year ago

#291 - ssUtils.py gtfToSSBed crashes if gtf doesn't have transcript_id

Issue - State: closed - Opened by diekhans over 1 year ago - 1 comment

#290 - flair correct crash with AttributeError: 'bool' object has no attribute 'find_overlap'

Issue - State: closed - Opened by diekhans over 1 year ago - 1 comment

#289 - Refactor - improved error messaging

Pull Request - State: closed - Opened by Jeltje over 1 year ago

#288 - The results of my test_output are not consisitent with the oferred test_expected. Why?

Issue - State: closed - Opened by qingwangchen over 1 year ago - 1 comment

#287 - Refactor

Pull Request - State: closed - Opened by Jeltje over 1 year ago

#286 - Refactor

Pull Request - State: closed - Opened by Jeltje over 1 year ago

#285 - diff_iso_usage documentation does not clear describe what it does

Issue - State: open - Opened by diekhans over 1 year ago

#284 - merging of transcript ids and gene ids is frustrating to use

Issue - State: closed - Opened by diekhans over 1 year ago - 2 comments

#283 - diff_iso_usage does not include header in output files

Issue - State: open - Opened by diekhans over 1 year ago

#282 - diffsplice_fishers_exact generates bogus error if input file is missing

Issue - State: open - Opened by diekhans over 1 year ago - 1 comment

#281 - `'run_id' is not defined` error while running `collapse-range`

Issue - State: closed - Opened by lvclark over 1 year ago - 2 comments

#280 - flair collapse creates invalid isoforms names that cause GTF conversion to fail

Issue - State: closed - Opened by diekhans over 1 year ago
Labels: bug

#279 - can't keep intermediate files when calling correct from flair

Issue - State: open - Opened by diekhans over 1 year ago - 1 comment
Labels: enhancement

#278 - accept BED9 as well as BED6 for splice junctions

Issue - State: open - Opened by diekhans over 1 year ago
Labels: enhancement

#277 - FLAIR need obvious succes or failure message

Issue - State: closed - Opened by diekhans over 1 year ago - 2 comments

#276 - FLAIR logging is very hard to use

Issue - State: open - Opened by diekhans over 1 year ago

#275 - FLAIR silently continues if no short read junctions are added

Issue - State: open - Opened by diekhans over 1 year ago

#274 - flair correct claims success even when there is an error

Issue - State: open - Opened by diekhans over 1 year ago

#273 - Please do not guess file types

Issue - State: open - Opened by diekhans over 1 year ago - 1 comment

#272 - junctions_from_sam creates invalid BEDs that are silently ignored

Issue - State: closed - Opened by diekhans over 1 year ago - 5 comments
Labels: bug

#271 - flair 123 appears not to use splice junctions

Issue - State: closed - Opened by diekhans over 1 year ago - 1 comment

#270 - flair correct documention doesn't define what <prefix>_ is

Issue - State: open - Opened by diekhans over 1 year ago

#269 - flair 123 is horribly hard to use

Issue - State: open - Opened by diekhans over 1 year ago - 1 comment

#268 - alarming "errors" when running multiple modules

Issue - State: open - Opened by diekhans over 1 year ago

#267 - Error while running collapse

Issue - State: closed - Opened by kundariyahardik over 1 year ago - 3 comments

#266 - diffsplice output format not documented

Issue - State: open - Opened by diekhans over 1 year ago

#265 - Questions about flair collapse in regards of TSS/TES calling algorithm

Issue - State: open - Opened by seungbeom-han over 1 year ago - 3 comments

#264 - Identification of full-length intergenic isoform

Issue - State: closed - Opened by Dongxu-Zheng over 1 year ago - 1 comment

GitHub / BrooksLabUCSC/flair issues and pull requests