GoekeLab bambu issues - Githubissues

GoekeLab / bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

GNU General Public License v3.0

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Merging qname from BAM file to readId.x

#435 hannalee809 opened 3 days ago
2
Bambu could not tell the gene id right from the input gtf file

#434 abcdtree closed 4 days ago
3
Fusion gene analysis?

#433 apsteinberg opened 1 week ago
4
read assignment data clarification

#432 sparthib closed 1 week ago
1
Use with prokaryotes to ID operons(?)

#431 kneubehl closed 1 week ago
2
multiple entries with the same exon_number for a given transcript_id

#430 zhangkn3 opened 1 month ago
1
Error in left_join(refGeneTxMap, dplyr::rename(refGeneTxMap, newGeneId.merge = newGeneId), : This join would result in more rows than dplyr can handle.

#429 dudududu12138 closed 3 weeks ago
3
How to use bambu in parellel on HPC clusters?

#428 dudududu12138 opened 1 month ago
0
Quantification of Transposable elements and/or chimeric TE-gene splice variants

#427 Kiliankleemann closed 1 month ago
3
NDR and novelTranscript columns do not exist in mcols(se)

#426 abcdtree closed 1 month ago
4
Clarification on `reads` argument

#425 cjw85 opened 2 months ago
2
mouse data

#424 mocherry opened 2 months ago
1
Error between bam and genome before extending annotations in precise locations

#423 BerrocalRubio333 closed 2 months ago
9
Transcripts identified by Bambu have a CPM or count value of 0 in all samples

#422 yuyun-zhang closed 1 month ago
13
question on multisampling

#421 sparthib opened 2 months ago
8
Is Bambu suitable for PB Kinnex?

#420 Tang-pro opened 2 months ago
2
Is Bambu suitable for PB Kinnex?

#419 Tang-pro closed 2 months ago
0
recommended quality control for input BAM files

#418 sparthib opened 3 months ago
1
Barcode demultiplexing on the long-reads alignment?

#417 ShaowenJ opened 3 months ago
4
Errors and warnings explanation

#416 zhangkn3 opened 3 months ago
2
Interpreting warning messages in discovery only mode

#415 sparthib opened 4 months ago
2
BiocParallel error when putting multiple .bam files as inputs for reads

#414 TingQi2020 opened 4 months ago
1
question about transcriptome/genome

#413 huawen-poppy opened 5 months ago
2
" double free or corruption (!prev) " when Start isoform quantification

#412 mechealeth closed 5 months ago
7
why multiple .bam files(>=7) cannot work

#411 Yumy526 opened 5 months ago
14
The same transcript with different counts in counts_transcript.txt

#410 thegreatFANG closed 5 months ago
3
singe exon transcript strand cDNA versus direct RNA nanopore protocol

#409 tderrien opened 5 months ago
2
dplyr::summarise message

#408 mikelove opened 5 months ago
0
XGBoost model serializaiton message

#407 mikelove opened 5 months ago
0
fixing the chunk when showing the import from the TxDb object

#406 federicomarini opened 6 months ago
0
de novo mode error

#405 haydenji0731 closed 6 months ago
4
Using pre-trained model vs de-novo transcript discovery

#404 apsteinberg closed 6 months ago
10
A few transcripts without strand infomation in the extended_annotations.gtf

#403 creaturemoon closed 7 months ago
4
Explanation of txClassDescriptions and error message for large bam file.

#402 apsteinberg closed 1 week ago
24
fix overcounting issue for incompatible counts

#401 cying111 closed 3 months ago
1
Quantifying precision and sensitivity of bambu using spike in data

#400 apsteinberg closed 8 months ago
4
can you guys make bambu run on command line

#398 yuukiiwa opened 8 months ago
0
Isofrom quantification Error: median(): detected NaN

#397 TingQi2020 closed 8 months ago
0
bambu command not recognized

#396 dvirdi01 closed 8 months ago
4
Incomplete result from minimap2-aligned bam files

#395 zhangkn3 closed 8 months ago
19
The deprecated feature was likely used in the bambu package

#394 alexander-schl closed 9 months ago
3
Discrepancy gene counts (bambu) with less and more sequencing depth

#393 NikoLichi closed 8 months ago
6
Including bambu annotation/GRanges for DEXSeq

#391 rugilemat closed 8 months ago
1
Request: Provide a container

#390 andreas-wilm closed 10 months ago
2
Don't compress gene assignments before fusion assignment

#389 andredsim opened 10 months ago
1
Fix crash when no warnings from bam

#388 andredsim closed 10 months ago
1
Subsetting annotation for protein_coding biotypes

#387 kenneditodd closed 8 months ago
2
Update XGboost models for new version

#386 andredsim opened 11 months ago
1
Failed to find a rowRanges() method for CompressedGRangesList objects.

#385 alexyfyf closed 11 months ago
4
Bug fix plot bambu

#384 cying111 opened 11 months ago
1