Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / bcgsc/rna-bloom issues and pull requests

#82 - BoundsException

Issue - State: open - Opened by YIGUIz 4 months ago - 1 comment

#81 - DBG construction from short and long reads

Issue - State: open - Opened by SimonHegele 5 months ago - 2 comments
Labels: question

#80 - About multi-tissue assembly

Issue - State: open - Opened by YIGUIz 5 months ago - 8 comments
Labels: question

#78 - Error assembling long read PacBio, no overlaps

Issue - State: open - Opened by A-pcd 6 months ago - 3 comments
Labels: question

#77 - Best practices for pre-processing prior to assembly

Issue - State: open - Opened by patrickaoude 7 months ago - 6 comments
Labels: question

#76 - Long reads genome guided

Issue - State: open - Opened by sagnikbanerjee15 7 months ago - 1 comment
Labels: question

#75 - is the assembly deterministic?

Issue - State: closed - Opened by alexyfyf 7 months ago - 3 comments
Labels: question

#73 - assembling nanopore sequenced bacterial transcriptomes

Issue - State: open - Opened by bioinfo17 9 months ago - 1 comment
Labels: question

#72 - error in assembling ONT DRS long reads

Issue - State: open - Opened by nmrt-sahu 9 months ago - 1 comment
Labels: question

#71 - reduce redundancy in direct RNA long-read only assembly?

Issue - State: open - Opened by mjudd8 10 months ago - 1 comment
Labels: question

#70 - Consensus transcriptome de novo with multiple samples

Issue - State: open - Opened by nriareal 10 months ago - 1 comment
Labels: question

#69 - RAM requirements. What is the minimum?

Issue - State: closed - Opened by nriareal 11 months ago - 2 comments
Labels: question

#68 - Question about assemble long-read sequencing data with short-read polishing

Issue - State: open - Opened by huawen-poppy about 1 year ago - 3 comments
Labels: question

#67 - Can output be used for DE analysis?

Issue - State: closed - Opened by kzudock about 1 year ago - 2 comments
Labels: question

#66 - Resolve Racon Conflict with Numeric Named Reads

Pull Request - State: open - Opened by ad3002 about 1 year ago - 3 comments

#65 - question about the output

Issue - State: closed - Opened by huawen-poppy about 1 year ago - 2 comments
Labels: question

#64 - can rnabloom run from stage 3?

Issue - State: closed - Opened by huawen-poppy about 1 year ago - 2 comments
Labels: question

#63 - Errors (reading file and I/O) for one of 9 pooled assemblies

Issue - State: closed - Opened by tonyaseverson over 1 year ago - 11 comments
Labels: question

#62 - RNABloom not creating transcriptome files

Issue - State: closed - Opened by dvirdi01 over 1 year ago - 3 comments
Labels: question

#61 - Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Issue - State: closed - Opened by nityendra21 over 1 year ago - 4 comments
Labels: question

#60 - Java out of memory exception

Issue - State: closed - Opened by dvirdi01 over 1 year ago - 3 comments
Labels: question

#59 - Inputting multiple long-read files at once

Issue - State: closed - Opened by dvirdi01 over 1 year ago - 3 comments
Labels: question

#58 - conda install url not working

Issue - State: closed - Opened by dvirdi01 over 1 year ago - 1 comment
Labels: question

#57 - Transcriptome assembly from ONT direct RNA sequencing seems to be incomplete

Issue - State: closed - Opened by OliviaAgatha over 1 year ago - 9 comments
Labels: question

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

Issue - State: closed - Opened by alexander-ahn over 1 year ago - 4 comments
Labels: question

#55 - Improve hairpin/palindrome removal in long-read assembly

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

#54 - Output error message for pooled assembly of single-end reads

Issue - State: open - Opened by kmnip over 1 year ago
Labels: bug

#53 - questions about how to get genes from the output

Issue - State: open - Opened by alexyfyf over 1 year ago - 4 comments
Labels: enhancement, question

#52 - RNA-Bloom2 version

Issue - State: closed - Opened by ARW-UBT almost 2 years ago - 1 comment
Labels: question

#52 - RNA-Bloom2 version

Issue - State: closed - Opened by ARW-UBT almost 2 years ago - 1 comment
Labels: question

#51 - Feature request: long-read reference-guided assembly

Issue - State: open - Opened by oneillkza over 2 years ago
Labels: enhancement

#50 - ERROR: Error during redundancy reduction!

Issue - State: closed - Opened by xiekunwhy over 2 years ago - 1 comment
Labels: bug

#49 - Problem parsing fasta file

Issue - State: closed - Opened by JC-therea over 2 years ago - 3 comments
Labels: enhancement

#48 - RNA-Bloom Generates Empty FASTA Without Error

Issue - State: closed - Opened by schorlton over 2 years ago - 8 comments
Labels: bug

#47 - Feature Request: More verbose logging?

Issue - State: closed - Opened by schorlton over 2 years ago - 1 comment
Labels: enhancement

#46 - Transcript headers follow different formats

Issue - State: closed - Opened by schorlton over 2 years ago - 3 comments
Labels: enhancement

#45 - Fix bug when read names contain `/`

Issue - State: closed - Opened by kmnip over 2 years ago
Labels: bug

#44 - ERROR: Incorrect FASTA header format

Issue - State: closed - Opened by schorlton over 2 years ago - 1 comment
Labels: bug

#43 - ERROR: For input string: "9223372036854775808"

Issue - State: closed - Opened by schorlton over 2 years ago - 6 comments
Labels: bug

#42 - ERROR: Infinite or NaN

Issue - State: closed - Opened by schorlton over 2 years ago - 5 comments
Labels: bug

#41 - We really need to keep E0.L. sequence?

Issue - State: closed - Opened by xiekunwhy almost 3 years ago - 3 comments
Labels: question

#40 - Release memory before redundancy reducing step.

Issue - State: closed - Opened by xiekunwhy almost 3 years ago - 5 comments
Labels: enhancement

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

Issue - State: closed - Opened by xiekunwhy almost 3 years ago - 9 comments
Labels: question

#38 - instruction about the output file

Issue - State: closed - Opened by zhaocheng3326 almost 3 years ago - 1 comment

#37 - Assemble multipple bulk RNA samples

Issue - State: closed - Opened by xiekunwhy almost 3 years ago - 3 comments
Labels: question

#36 - Improved README: Add output files description

Issue - State: closed - Opened by Ebedthan almost 3 years ago - 2 comments
Labels: enhancement

#35 - How to restart a failed run

Issue - State: closed - Opened by jesgomez almost 3 years ago - 1 comment
Labels: question

#34 - 3'UTR transgene identification from 10x scRNAseq reads

Issue - State: closed - Opened by auesro about 3 years ago - 36 comments
Labels: question

#33 - FastQ gzipped files not accepted as input?

Issue - State: closed - Opened by auesro about 3 years ago - 8 comments

#20 - How to remove the isoform in the trasncript.fa file?

Issue - State: closed - Opened by mathavanpu about 3 years ago - 3 comments
Labels: question

#19 - Coverage does not add up

Issue - State: closed - Opened by schorlton over 3 years ago - 4 comments
Labels: question

#18 - c=null in output FASTA

Issue - State: closed - Opened by schorlton over 3 years ago - 7 comments
Labels: bug

#16 - Output doubts single-cell RNA-seq assembly

Issue - State: closed - Opened by MartaBenegas about 4 years ago - 10 comments
Labels: question

#15 - Running time

Issue - State: closed - Opened by jlim125 about 4 years ago - 14 comments

#14 - Sequence header

Issue - State: closed - Opened by giantoni over 4 years ago - 5 comments
Labels: question

#13 - Execution halted at mergepool stage

Issue - State: closed - Opened by KristinaGagalova over 4 years ago - 3 comments

#12 - Filter output by coverage?

Issue - State: closed - Opened by xuesoso over 4 years ago - 1 comment
Labels: question

#11 - Error with conda installation

Issue - State: closed - Opened by KristinaGagalova over 4 years ago - 4 comments

#10 - Error occur during RNA-Bloom command

Issue - State: closed - Opened by aman21392 over 4 years ago - 1 comment

#9 - null exception

Issue - State: closed - Opened by dschwoerer over 4 years ago - 4 comments

#8 - Error assembling long reads

Issue - State: closed - Opened by sum732 over 4 years ago - 24 comments
Labels: help wanted

#7 - Correct Strand Information and Pairing

Issue - State: closed - Opened by sum732 over 4 years ago - 1 comment
Labels: question

#6 - Racon Installation

Issue - State: closed - Opened by sum732 over 4 years ago - 2 comments

#5 - Illumina PE (Stranded) and PacBio Reads for RNA-Seq

Issue - State: closed - Opened by sum732 over 4 years ago - 4 comments
Labels: question

#4 - Program doesn't finish on tiny test dataset (illumina PE & ONP)

Issue - State: closed - Opened by lmuenter almost 5 years ago - 3 comments
Labels: bug

#3 - Reg: Normalization of PE datasets

Issue - State: closed - Opened by harish0201 almost 5 years ago - 4 comments
Labels: question

#2 - Question: De-novo assembly of long reads ONLY - Java memory error

Issue - State: closed - Opened by sid5427 about 5 years ago - 18 comments
Labels: bug, question

#1 - FastqReader Error?

Issue - State: closed - Opened by Atalasia over 5 years ago - 9 comments
Labels: bug