bcgsc/RNA-Bloom

Issues

• Best practices for pre-processing prior to assembly

  #77 opened 2 months ago by patrickaoude
  6

• ERROR: Error during redundancy reduction!

  #50 opened a month ago by xiekunwhy
  1

• RAM requirements. What is the minimum?

  #69 opened a month ago by nriareal
  2

• RNABloom not creating transcriptome files

  #62 opened a month ago by dvirdi01
  3

• Java out of memory exception

  #60 opened a month ago by dvirdi01
  3

• Inputting multiple long-read files at once

  #59 opened a month ago by dvirdi01
  3

• Transcriptome assembly from ONT direct RNA sequencing seems to be incomplete

  #57 opened a month ago by OliviaAgatha
  9

• Containerized rnabloom returning "Unsupported file format detected" error for fastq.gz files when used with Nextflow

  #79 opened a month ago by tonyaseverson
  2

• Error assembling long read PacBio, no overlaps

  #78 opened 2 months ago by A-pcd
  3

• Long reads genome guided

  #76 opened 2 months ago by sagnikbanerjee15
  1

• is the assembly deterministic?

  #75 opened 2 months ago by alexyfyf
  3

• Improving Sensitivity for Similar Isoform Assembly and Handling PacBio HiFi RNA Reads Without Polishing

  #74 opened 3 months ago by zhenyu7500
  3

• assembling nanopore sequenced bacterial transcriptomes

  #73 opened 4 months ago by bioinfo17
  1

• error in assembling ONT DRS long reads

  #72 opened 5 months ago by nmrt-sahu
  1

• reduce redundancy in direct RNA long-read only assembly?

  #71 opened 5 months ago by mjudd8
  1

• Consensus transcriptome de novo with multiple samples

  #70 opened 5 months ago by nriareal
  1

• Question about assemble long-read sequencing data with short-read polishing

  #68 opened 8 months ago by huawen-poppy
  3

• question about the output

  #65 opened 8 months ago by huawen-poppy
  2

• Can output be used for DE analysis?

  #67 opened 8 months ago by kzudock
  2

• can rnabloom run from stage 3?

  #64 opened 10 months ago by huawen-poppy
  2

• Errors (reading file and I/O) for one of 9 pooled assemblies

  #63 opened 10 months ago by tonyaseverson
  11

• Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

  #61 opened a year ago by nityendra21
  4

• conda install url not working

  #58 opened a year ago by dvirdi01
  1

• Coverage does not add up

  #19 opened a year ago by schorlton
  4

• How to remove the isoform in the trasncript.fa file?

  #20 opened a year ago by mathavanpu
  3

• RNA-Bloom2 version

  #52 opened a year ago by ARW-UBT
  1

• How to restart a failed run

  #35 opened a year ago by jesgomez
  1

• Q. Error in extracting unique reads at Stage 3 (Assembling long reads for "rnabloom")

  #56 opened a year ago by alexander-ahn
  4

• Improve hairpin/palindrome removal in long-read assembly

  #55 opened a year ago by kmnip
  0

• questions about how to get genes from the output

  #53 opened a year ago by alexyfyf
  4

• Output error message for pooled assembly of single-end reads

  #54 opened a year ago by kmnip
  0

• Transcript headers follow different formats

  #46 opened 2 years ago by schorlton
  3

• Fix bug when read names contain `/`

  #45 opened 2 years ago by kmnip
  0

• ERROR: For input string: "9223372036854775808"

  #43 opened 2 years ago by schorlton
  6

• Problem parsing fasta file

  #49 opened 2 years ago by JC-therea
  3

• RNA-Bloom Generates Empty FASTA Without Error

  #48 opened 2 years ago by schorlton
  8

• Feature Request: More verbose logging?

  #47 opened 2 years ago by schorlton
  1

• Feature request: long-read reference-guided assembly

  #51 opened 2 years ago by oneillkza
  0

• ERROR: Incorrect FASTA header format

  #44 opened 2 years ago by schorlton
  1

• ERROR: Infinite or NaN

  #42 opened 2 years ago by schorlton
  5

• Release memory before redundancy reducing step.

  #40 opened 2 years ago by xiekunwhy
  5

• Improved README: Add output files description

  #36 opened 2 years ago by Ebedthan
  2

• c=null in output FASTA

  #18 opened 2 years ago by schorlton
  7

• We really need to keep E0.L. sequence?

  #41 opened 2 years ago by xiekunwhy
  3

• Assemble multipple bulk RNA samples

  #37 opened 2 years ago by xiekunwhy
  3

• 3'UTR transgene identification from 10x scRNAseq reads

  #34 opened 2 years ago by auesro
  36

• java.lang.RuntimeException: java.lang.StringIndexOutOfBoundsException: String index out of range: -1

  #39 opened 3 years ago by xiekunwhy
  9

• instruction about the output file

  #38 opened 3 years ago by zhaocheng3326
  1

• FastQ gzipped files not accepted as input?

  #33 opened 3 years ago by auesro
  8

• Output doubts single-cell RNA-seq assembly

  #16 opened 3 years ago by MartaBenegas
  10