pachterlab kallistobustools issues

pachterlab / kallistobustools

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

https://kallistobus.tools/

MIT License

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issues

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Extracting Transcript-Level Counts from Single-Nuclei Data for DTE/DTU Analysis

#63 AkilaRanjith opened 4 months ago
0
Error while quantifying with multi-mapping (-mm) option

#62 jaiganeshjg closed 5 months ago
1
.h5ad file does not contain layers spliced and unspliced

#61 mdu4003 opened 6 months ago
2
Error: Number of files (1) does not match number of input files required by technology 10XV1 (3)

#60 Gabrisfon opened 8 months ago
14
How to specify filtered barcodes to generate a loom file?

#59 micosacak opened 8 months ago
0
kb count error with CSP reads

#58 kaijli closed 5 months ago
0
Issue with kb count

#57 lucasinchausti opened 10 months ago
3
Error: gtf argument when running kb ref: FileNotFoundError: [Errno 2] No such file or directory: 'gtf'

#56 McKSal closed 1 year ago
5
Improving speed when running `kb count`

#55 reetm09 opened 1 year ago
3
Verifying status of "uniqueness" of alignments for single cell analysis

#54 sknaack opened 1 year ago
0
Running time

#53 BenjaminDEMAILLE opened 1 year ago
0
issue with pip install kb-python

#52 dsmolina opened 1 year ago
0
how to implement EM using kb?

#51 jc271828 opened 1 year ago
2
Why is there a big difference between kallisto and cellranger count result？

#50 aizhimin opened 1 year ago
6
kb count subprocess.CalledProcessError:

#49 victorcat4 closed 1 year ago
2
How to get isoform counts for single cell RNA-seq data?

#48 biopzhang opened 2 years ago
3
Recommendation for alignment visualization

#47 jkniehaus opened 2 years ago
1
What should I do if the gene name is empty when I set "--cellranger" parm

#46 dylenchang opened 2 years ago
0
kallisto bustools with reference transcriptome

#45 MartaBenegas opened 2 years ago
5
kb ref returns empty 'to be generated' files

#44 liliay closed 2 years ago
9
SRA Downloads a Single FASTQ File for Paired-End Reads Which Is Not Compatible with Kallisto Workflow

#43 erguntiryaki opened 2 years ago
0
Nucleus workflow for RNA Velocity - no spliced/unspliced layers in file output

#42 AlinaKurjan closed 2 years ago
1
update deprecated --lamanno option with the --workflow lamanno option

#41 erguntiryaki closed 1 week ago
1
Mito genes not having '-' in the t2g.txt

#40 GabyBG closed 2 years ago
5
RNA Velocity

#39 FionaMoon opened 2 years ago
0
Required files for technology = smartseq2

#38 ostkampp opened 2 years ago
3
How to provide read1 and read2 fastq files from two lanes to `kb count`?

#37 naity2 closed 2 years ago
2
Rhapsody addition?

#36 theheking opened 2 years ago
3
Quantify ARC-v1 data

#35 ChristopherBarrington opened 2 years ago
1
Hardcoded whitelists

#34 apredeus closed 2 years ago
5
RNA velocity similar mtx for spliced and unspliced region (dropseq)

#33 AkilaRanjith closed 2 years ago
0
How to filter/subset cells for RNA Velocity from kb?

#32 SimoniMD closed 2 years ago
1
Cannot install kb using pip

#30 ekernf01 closed 2 years ago
2
Problem running kb count w/ multiple intron files

#29 stmartineau closed 2 years ago
2
Splitting multimapping read with EM algorithm

#28 joycekang closed 3 years ago
2
Visium tutorial

#27 lambdamoses opened 3 years ago
1
Different splice abundances than kb tutorial

#25 carbycrab opened 3 years ago
0
error message tracing back to get_kallisto_version

#24 sanjayrsrivatsan closed 3 years ago
1
mitochondrial gene filtering

#21 AuroreCapillon opened 3 years ago
0
Keyboard interrupt error

#20 kdhkiani closed 3 years ago
0
0 reads pseudoaligned[~warn] no reads pseudoaligned

#19 kaizen89 closed 3 years ago
2
How does Kallisto bus tools handle multi-mapping reads?

#15 kikegoni closed 4 years ago
6
How to specify -x with a new technology

#14 ogandril closed 4 years ago
2
kallistobus for MARSseq data

#13 ogandril closed 4 years ago
3
Multiple sequensing runs

#12 mariafiruleva closed 4 years ago
2
kallisto bus is not avaialble

#11 liu-xingliang closed 4 years ago
1
URL Down

#10 YogiOnBioinformatics closed 4 years ago
3
Pearson correlation is low and many marker genes are not detected when I used the pbmc1k v3 dataset

#9 qizhengyang2017 closed 4 years ago
23
RNA isoform/alternative splicing analysis

#8 grimwoo opened 4 years ago
5
kallisto rna velocity RCPP issue

#7 yaolutian closed 4 years ago
3