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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Help replicating results from another paper

#453 NikoLichi opened 1 week ago
3
Multiplex_Major_Patch

#452 andredsim opened 4 weeks ago
0
Fix typo in extendAnnotations

#451 andredsim closed 4 weeks ago
0
Large numebr of BAM files leads to Error in `vec_interleave_indices()`:

#450 NikoLichi opened 1 month ago
10
BiocParallel error when using Bambu in quantification mode

#449 apsteinberg opened 2 months ago
0
Merging read classes across samples results in fewer novel transcripts

#448 apsteinberg opened 2 months ago
14
Error in xgb.get.handle(object): 'xgb.Booster' object is corrupted or is from an incompatible xgboost version.

#447 nick-youngblut opened 2 months ago
6
Input genome file not readable => bambu does not support gzip'd input

#446 nick-youngblut opened 2 months ago
5
read assignment information

#445 sparthib opened 2 months ago
4
Merging transcript gtfs across multiple samples

#444 apsteinberg closed 2 months ago
5
Low increase in discovered isoforms with RNA004 data

#443 dietvin opened 3 months ago
1
Best minimap2 parameters for use with bambu

#442 rob-p closed 3 months ago
2
Transcripts identified by Bambu have a CPM or count value of 0 in all samples

#441 alexyfyf opened 4 months ago
2
inconsistent gene and transcript count

#440 alexyfyf closed 4 months ago
2
How to improve the efficiency on a single sample?

#439 dudududu12138 opened 4 months ago
3
How to extract transcript assembled from the RNA-seq data?

#438 dudududu12138 closed 4 months ago
5
Differences between uniqueCounts_transcript.txt and readToTranscriptMaps

#437 camelest closed 4 months ago
4
Make novel GTF from single cell data using bambu

#436 hyeon9 closed 4 months ago
1
Merging qname from BAM file to readId.x

#435 hannalee809 closed 4 months ago
4
Bambu could not tell the gene id right from the input gtf file

#434 abcdtree closed 5 months ago
3
Fusion gene analysis?

#433 apsteinberg opened 5 months ago
6
read assignment data clarification

#432 sparthib closed 5 months ago
1
Use with prokaryotes to ID operons(?)

#431 kneubehl closed 5 months ago
2
multiple entries with the same exon_number for a given transcript_id

#430 zhangkn3 opened 5 months 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 5 months ago
3
How to use bambu in parellel on HPC clusters?

#428 dudududu12138 opened 6 months ago
1
Quantification of Transposable elements and/or chimeric TE-gene splice variants

#427 Kiliankleemann closed 6 months ago
3
NDR and novelTranscript columns do not exist in mcols(se)

#426 abcdtree closed 6 months ago
4
Clarification on `reads` argument

#425 cjw85 opened 7 months ago
2
mouse data

#424 mocherry opened 7 months ago
1
Error between bam and genome before extending annotations in precise locations

#423 BerrocalRubio333 closed 7 months ago
9
Transcripts identified by Bambu have a CPM or count value of 0 in all samples

#422 yuyun-zhang closed 6 months ago
13
question on multisampling

#421 sparthib opened 7 months ago
8
Is Bambu suitable for PB Kinnex?

#420 Tang-pro closed 4 months ago
2
Is Bambu suitable for PB Kinnex?

#419 Tang-pro closed 7 months ago
0
recommended quality control for input BAM files

#418 sparthib opened 8 months ago
1
Barcode demultiplexing on the long-reads alignment?

#417 ShaowenJ opened 8 months ago
4
Errors and warnings explanation

#416 zhangkn3 opened 8 months ago
2
Interpreting warning messages in discovery only mode

#415 sparthib opened 8 months ago
2
BiocParallel error when putting multiple .bam files as inputs for reads

#414 TingQi2020 opened 8 months ago
1
question about transcriptome/genome

#413 huawen-poppy opened 10 months ago
2
" double free or corruption (!prev) " when Start isoform quantification

#412 mechealeth closed 10 months ago
7
why multiple .bam files(>=7) cannot work

#411 Yumy526 opened 10 months ago
14
The same transcript with different counts in counts_transcript.txt

#410 thegreatFANG closed 10 months ago
3
singe exon transcript strand cDNA versus direct RNA nanopore protocol

#409 tderrien opened 10 months ago
2
dplyr::summarise message

#408 mikelove opened 10 months ago
0
XGBoost model serializaiton message

#407 mikelove opened 10 months ago
0
fixing the chunk when showing the import from the TxDb object

#406 federicomarini opened 11 months ago
0
de novo mode error

#405 haydenji0731 closed 11 months ago
4
Using pre-trained model vs de-novo transcript discovery

#404 apsteinberg closed 11 months ago
10