GoekeLab/bambu

Issues

• Help replicating results from another paper

  #453 opened a month ago by NikoLichi
  3

• Large numebr of BAM files leads to Error in `vec_interleave_indices()`:

  #450 opened 2 months ago by NikoLichi
  10

• Merging read classes across samples results in fewer novel transcripts

  #448 opened 3 months ago by apsteinberg
  14

• read assignment information

  #445 opened 4 months ago by sparthib
  4

• Input genome file not readable => bambu does not support gzip'd input

  #446 opened 3 months ago by nick-youngblut
  5

• Error in xgb.get.handle(object): 'xgb.Booster' object is corrupted or is from an incompatible xgboost version.

  #447 opened 3 months ago by nick-youngblut
  6

• BiocParallel error when using Bambu in quantification mode

  #449 opened 3 months ago by apsteinberg
  0

• Merging transcript gtfs across multiple samples

  #444 opened 4 months ago by apsteinberg
  5

• Low increase in discovered isoforms with RNA004 data

  #443 opened 4 months ago by dietvin
  1

• Best minimap2 parameters for use with bambu

  #442 opened 5 months ago by rob-p
  2

• Transcripts identified by Bambu have a CPM or count value of 0 in all samples

  #441 opened 6 months ago by alexyfyf
  2

• Is Bambu suitable for PB Kinnex?

  #420 opened 5 months ago by Tang-pro
  2

• How to use bambu in parellel on HPC clusters?

  #428 opened 7 months ago by dudududu12138
  1

• Make novel GTF from single cell data using bambu

  #436 opened 5 months ago by hyeon9
  1

• How to improve the efficiency on a single sample?

  #439 opened 6 months ago by dudududu12138
  3

• How to extract transcript assembled from the RNA-seq data?

  #438 opened 6 months ago by dudududu12138
  5

• inconsistent gene and transcript count

  #440 opened 6 months ago by alexyfyf
  2

• Differences between uniqueCounts_transcript.txt and readToTranscriptMaps

  #437 opened 6 months ago by camelest
  4

• Fusion gene analysis?

  #433 opened 6 months ago by apsteinberg
  6

• Merging qname from BAM file to readId.x

  #435 opened 6 months ago by hannalee809
  4

• Bambu could not tell the gene id right from the input gtf file

  #434 opened 6 months ago by abcdtree
  3

• Explanation of txClassDescriptions and error message for large bam file.

  #402 opened 6 months ago by apsteinberg
  24

• Use with prokaryotes to ID operons(?)

  #431 opened 6 months ago by kneubehl
  2

• read assignment data clarification

  #432 opened 6 months ago by sparthib
  1

• Error in left_join(refGeneTxMap, dplyr::rename(refGeneTxMap, newGeneId.merge = newGeneId), : This join would result in more rows than dplyr can handle.

  #429 opened 7 months ago by dudududu12138
  3

• multiple entries with the same exon_number for a given transcript_id

  #430 opened 7 months ago by zhangkn3
  1

• Quantification of Transposable elements and/or chimeric TE-gene splice variants

  #427 opened 7 months ago by Kiliankleemann
  3

• Transcripts identified by Bambu have a CPM or count value of 0 in all samples

  #422 opened 7 months ago by yuyun-zhang
  13

• NDR and novelTranscript columns do not exist in mcols(se)

  #426 opened 8 months ago by abcdtree
  4

• Clarification on `reads` argument

  #425 opened 8 months ago by cjw85
  2

• Error between bam and genome before extending annotations in precise locations

  #423 opened 8 months ago by BerrocalRubio333
  9

• question on multisampling

  #421 opened 9 months ago by sparthib
  8

• mouse data

  #424 opened 9 months ago by mocherry
  1

• Is Bambu suitable for PB Kinnex?

  #419 opened 9 months ago by Tang-pro
  0

• Barcode demultiplexing on the long-reads alignment?

  #417 opened 9 months ago by ShaowenJ
  4

• recommended quality control for input BAM files

  #418 opened 9 months ago by sparthib
  1

• why multiple .bam files(>=7) cannot work

  #411 opened a year ago by Yumy526
  14

• Errors and warnings explanation

  #416 opened 10 months ago by zhangkn3
  2

• Interpreting warning messages in discovery only mode

  #415 opened 10 months ago by sparthib
  2

• BiocParallel error when putting multiple .bam files as inputs for reads

  #414 opened 10 months ago by TingQi2020
  1

• " double free or corruption (!prev) " when Start isoform quantification

  #412 opened a year ago by mechealeth
  7

• question about transcriptome/genome

  #413 opened a year ago by huawen-poppy
  2

• The same transcript with different counts in counts_transcript.txt

  #410 opened a year ago by thegreatFANG
  3

• singe exon transcript strand cDNA versus direct RNA nanopore protocol

  #409 opened a year ago by tderrien
  2

• XGBoost model serializaiton message

  #407 opened a year ago by mikelove
  0

• dplyr::summarise message

  #408 opened a year ago by mikelove
  0

• Using pre-trained model vs de-novo transcript discovery

  #404 opened a year ago by apsteinberg
  10

• de novo mode error

  #405 opened a year ago by haydenji0731
  4

• A few transcripts without strand infomation in the extended_annotations.gtf

  #403 opened a year ago by creaturemoon
  4

• Quantifying precision and sensitivity of bambu using spike in data

  #400 opened a year ago by apsteinberg
  4