MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software issues and pull requests

#144 - rna run报错

Issue - State: open - Opened by ExpertS04p 29 days ago - 11 comments

#143 - 无法生成spliced/unspliced RNA

Issue - State: closed - Opened by hyjforesight about 1 month ago - 3 comments

#142 - ValueError: truncated quality string in /home/bioyongjie/dnbc4tools_dataprocess/gxf_0011_1203/oligo/L01_1.fq.gz

Issue - State: open - Opened by Wu123453234 about 1 month ago - 1 comment

#141 - 只有bam文件如何使用dnbc4tools?

Issue - State: closed - Opened by hyjforesight about 1 month ago - 4 comments

#140 - 当scRNA-seq单样本有多个技术重复时，该如何运行命令？

Issue - State: closed - Opened by hyjforesight about 1 month ago - 6 comments

#139 - 单细胞分析时自动退出报错

Issue - State: open - Opened by ASasasdasfasfasfasfasf about 2 months ago - 8 comments

#138 - 关于GTF注释文件的格式

Issue - State: open - Opened by evewu2002 about 2 months ago - 3 comments

#137 - 关于同一样本多个文件如何编辑list文件> ```

Issue - State: open - Opened by evewu2002 about 2 months ago - 3 comments

#136 - 默认情况下rna run 结果是否包括内含子

Issue - State: closed - Opened by evewu2002 about 2 months ago - 2 comments

#135 - Sample data

Issue - State: open - Opened by Soft283 about 2 months ago - 1 comment

#134 - dnbc4tools removes lncRNA from the annotation file

Issue - State: open - Opened by Rohit-Satyam 2 months ago - 2 comments

#133 - feature.tsv文件中没有目标基因

Issue - State: open - Opened by lalune7 2 months ago - 6 comments

#132 - Provision to use custom regex for mitochondrial genes in non-human organism

Issue - State: closed - Opened by Rohit-Satyam 2 months ago - 4 comments

#131 - dnbc4tools rna run中断报错 Calculating bead similarity and merging beads

Issue - State: closed - Opened by anshrly 2 months ago - 1 comment

#130 - Can I use NCBI to construct a reference genome

Issue - State: open - Opened by xiaoying-codeLab 2 months ago - 1 comment

#129 - What is `output/attachment/RNAvelocity_matrix/spanning.mtx.gz` ?

Issue - State: closed - Opened by h4rvey-g 2 months ago - 3 comments

#128 - 如何在小鼠参考基因组基础上，构建一个带有EGFP基因或者其他非小鼠基因的参考基因组呢？How can we construct a reference genome with the EGFP gene or other non-mouse genes based on the mouse reference genome?

Issue - State: closed - Opened by XiaoRuipei2024edu 3 months ago - 6 comments

#127 - 其他物种参考基因组的构建

Issue - State: open - Opened by ASasasdasfasfasfasfasf 3 months ago - 9 comments

#126 - cDNA reads statistics bug?

Issue - State: open - Opened by liufuyan2016 3 months ago - 9 comments

#125 - Column C0 does not exist in the Frame

Issue - State: open - Opened by kinesin80s 3 months ago - 5 comments

#124 - Can't find a usable init.tcl in the following directories:

Issue - State: open - Opened by Rohit-Satyam 3 months ago - 2 comments

#123 - SATR options

Issue - State: open - Opened by KeiichiroKOIWAI 3 months ago - 2 comments

#122 - subprocess.CalledProcessError #returned non-zero exit status 139

Issue - State: open - Opened by binzhengbin 3 months ago - 29 comments

#121 - dnbc4tools 2.1.3 scATAC MACS2/IO/ScoreTrack...so: undefined symbol issue

Issue - State: open - Opened by lishuangshuang0616 3 months ago

#120 - 2.1.3

Pull Request - State: closed - Opened by lishuangshuang0616 4 months ago

#119 - 单细胞数据结果文件

Issue - State: open - Opened by ldan999 4 months ago - 5 comments

#118 - scRNA run结果解读

Issue - State: closed - Opened by ldan999 5 months ago - 3 comments

#117 - dnbc4tools installation issue

Issue - State: open - Opened by ErrolTian 5 months ago - 3 comments

#116 - Running the main workflow报错

Issue - State: closed - Opened by ldan999 5 months ago - 8 comments

#115 - 细胞数目和质量都很高

Issue - State: closed - Opened by LJIGDBLL 5 months ago - 5 comments

#114 - 关于dnbc4tools vdj run运行时间过长的咨询

Issue - State: closed - Opened by biginfor 5 months ago - 10 comments

#113 - How Does the Software Determine Beads Originate from the Same Cell?

Issue - State: open - Opened by lgchen-git 5 months ago - 3 comments

#112 - dnbc4tools4下载报错

Issue - State: open - Opened by ldan999 5 months ago - 2 comments

#111 - dnbc4toolsv2.0.7 install

Issue - State: open - Opened by qwccccc 5 months ago - 1 comment

#110 - Obtain transcript count matrics

Issue - State: open - Opened by hejian41 5 months ago - 4 comments

#109 - Concerns Regarding Differences Between V2.1.2 and V2.0.7 Pipelines

Issue - State: closed - Opened by Nh-code 5 months ago - 2 comments

#108 - 建立参考基因组索引问题

Issue - State: closed - Opened by ldan999 5 months ago - 3 comments

#107 - error: the following arguments are required: --name, --cDNAfastq1, --cDNAfastq2, --oligofastq1, --oligofastq2, --genomeDir

Issue - State: closed - Opened by ldan999 5 months ago - 2 comments

#106 - 构建参考基因组索引所需内存

Issue - State: closed - Opened by ldan999 5 months ago - 2 comments

#105 - 关于软件是否存在checkpoint机制的询问

Issue - State: closed - Opened by biginfor 5 months ago - 4 comments

#104 - Concerns Regarding "Sequencing Saturation" in the "DNBelab C4 scRNA-seq v2" Workflow Reports

Issue - State: closed - Opened by Nh-code 5 months ago - 2 comments

#103 - How to adjust `forceCellNum` for Optimal Cell Yield and Accuracy in the Pipline "DNBelab C4 scRNA-seq v2"

Issue - State: closed - Opened by Nh-code 5 months ago - 3 comments

#102 - dnbc4tools rna multi 不产生任何结果，但同时没有任何报错

Issue - State: closed - Opened by biginfor 5 months ago - 2 comments

#101 - C4单细胞上游分析样本存在多个文件

Issue - State: closed - Opened by ldan999 5 months ago - 6 comments

#100 - 如何使用 scanpy 读取 raw_matrix下的文件？

Issue - State: open - Opened by zhoutianrui-tongji 5 months ago - 4 comments

#99 - Output matrix with gene_id

Issue - State: open - Opened by ShuyangXu 5 months ago - 1 comment

#98 - 来自不同分析版本的样品

Issue - State: closed - Opened by LJIGDBLL 6 months ago - 2 comments

#97 - SAW-A10186 中途自动终止并报错。

Issue - State: open - Opened by LJIGDBLL 6 months ago - 1 comment

#96 - C4单细胞上游分析提问

Issue - State: open - Opened by hswl1314 6 months ago - 2 comments

#95 - 请问如何将bam文件进行上游分析

Issue - State: open - Opened by GGG622188 6 months ago - 3 comments

#94 - ERROR - similarity: main.c:369: create_index_array: Assertion `((infos)->n) > 0' failed.

Issue - State: open - Opened by yjzhang1020 6 months ago - 14 comments

#93 - NoDataError: empty CSV

Issue - State: open - Opened by peipp410 6 months ago - 6 comments

#92 - dnbc4tools run 报错 Error code: SAW-A10187

Issue - State: closed - Opened by sheny-bio 6 months ago - 8 comments

#91 - add Custom gene to Reference, but filtered out in GTF file after mkgtf

Issue - State: closed - Opened by zclecle2 6 months ago - 4 comments

#90 - DNBSEQ-T7 platform demultiplexing

Issue - State: open - Opened by Maple-sakura 6 months ago - 4 comments

#89 - 我该如何将结果文件读取到 python 中进行后续分析（包括 UMAP 和细胞类型注释）？（Scanpy）

Issue - State: closed - Opened by zhoutianrui-tongji 6 months ago - 2 comments

#88 - filter matrix 和 raw matrix有什么区别？

Issue - State: open - Opened by ultraypy 7 months ago - 3 comments

#87 - A question about multiple files of one sample

Issue - State: open - Opened by NJU-Bio-Info 7 months ago - 10 comments

#86 - Dnbc4 dev

Pull Request - State: closed - Opened by lishuangshuang0616 7 months ago

#85 - How to add a marker gene for building a custom reference for dnbc4tools?

Issue - State: closed - Opened by jiangjasson 7 months ago - 4 comments

#84 - ImportError:undefined symbol: BrotliSharedDictionaryDestroyInstance

Issue - State: closed - Opened by jiangjasson 7 months ago - 3 comments

#83 - dnbc4tools rna run 的时候报错：Signals.SIGABRT: 6

Issue - State: closed - Opened by YaoQiong1127 7 months ago - 18 comments

#82 - scATAC version 2.1.2 SIGNALS error description

Issue - State: open - Opened by lishuangshuang0616 8 months ago - 7 comments
Labels: bug

#81 - 请问注释的原理是什么

Issue - State: closed - Opened by ultraypy 8 months ago - 1 comment

#80 - subprocess.CalledProcessError

Issue - State: open - Opened by hullv 8 months ago - 5 comments

#79 - subprocess.CalledProcessError:

Issue - State: closed - Opened by hullv 8 months ago

#78 - how would you convert the output of dnbc2tools to count matrix

Issue - State: closed - Opened by sherry1000001 8 months ago - 8 comments

#77 - Command failed with exit code 255

Issue - State: closed - Opened by Arknights2 8 months ago - 9 comments

#76 - Exception: The chemistry and darkreaction are unable to be automatically determined.

Issue - State: closed - Opened by Xxhongs 8 months ago - 2 comments

#75 - 使用PE100模式测序是否适用DNBc4tools

Issue - State: closed - Opened by Tc940417 9 months ago - 2 comments

#74 - dnbc4tools rna run: Unable to find custom marker genes in the 02.count/features.tsv.gz file even they are appeared in the 01.data/final_sorted.bam

Issue - State: closed - Opened by zebrafishCC 9 months ago - 11 comments

#73 - Saturation problem

Issue - State: closed - Opened by hullv 9 months ago - 9 comments

#72 - ERROR when running dnbc4tools rna

Issue - State: closed - Opened by kobeho24 9 months ago - 13 comments

#71 - RNA velocity分析

Issue - State: closed - Opened by tyyl622 9 months ago - 6 comments

#70 - version 2.1.2

Pull Request - State: closed - Opened by lishuangshuang0616 9 months ago

#69 - Error in barcodeRanks(t(m), lower = 0.005) : insufficient unique points for computing knee/inflection points 2024-04-24

Issue - State: closed - Opened by hullv 9 months ago - 9 comments

#68 - 可以使用Soupx对dnbc4tools产生的raw_matrix和filter_matrix进行去环境RNA污染吗？

Issue - State: closed - Opened by kjHuoo 10 months ago - 2 comments

#67 - How does DNBC4tools calculate RNA velocity, and how can I use the results from RNAvelocity_matrix directory.

Issue - State: closed - Opened by yemao701 10 months ago - 4 comments

#66 - BGISEQ-500/DNBSEQ-T7 platform demultiplexing

Issue - State: closed - Opened by Maple-sakura 10 months ago - 3 comments

#65 - Error code: SAW-A10400, get signal: 18

Issue - State: closed - Opened by Tc940417 10 months ago - 11 comments

#64 - dnbc4tools atac run 运行报错

Issue - State: closed - Opened by Ruvic-chen 10 months ago - 7 comments

#63 - Error in .local(m, ...) : insufficient unique points for computing knee/inflection points

Issue - State: open - Opened by Tan-GuangHui 10 months ago - 4 comments

#62 - BAM file generated by DNBelab

Issue - State: closed - Opened by TianYu-828 11 months ago

#61 - DNBC4Tools产生的单细胞数据可以使用MARVEL进行RNA剪接分析吗？

Issue - State: closed - Opened by TianYu-828 12 months ago - 4 comments

#60 - 如何通过调整拐点调整细胞数目

Issue - State: open - Opened by momo0519 12 months ago - 3 comments

#59 - matrix.mtx.gz文件表头汇总信息中raw与filter matrix基因数和非零数值与行数不一致的问题

Issue - State: closed - Opened by antecede 12 months ago - 7 comments

#58 - dnbc4tools run 报错

Issue - State: open - Opened by owo12138 about 1 year ago - 38 comments

GitHub / MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software issues and pull requests