10XGenomics cellranger issues

10XGenomics / cellranger

10x Genomics Single Cell Analysis

https://www.10xgenomics.com/support/software/cell-ranger

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issues

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ERROR: No input FASTQs were found for the requested parameters.

#246 2124sa closed 1 month ago
1
is_cell and high_confidence columns

#245 Egl-A closed 2 months ago
1
Error in "cellranger mkref"

#244 grimwoo closed 3 months ago
1
matrix, features and barcode using `cellranger vdj` and `cellranger multi`

#243 malonzm1 closed 4 months ago
1
ERROR in running Cellranger multi for BEAM-T

#242 Esche-Hohenstein closed 5 months ago
1
UMI indel correction

#241 dakyung99 closed 6 months ago
2
Different ways to identify gtf format between version 7.0.0 and 7.2.0 of Cellranger

#240 lexuziandyu closed 6 months ago
1
merge 2 sequencing run of Multiplex FRP, 1 Probe Barcode/sample

#239 archana433 closed 7 months ago
1
Illegal instruction (core dumped)

#238 nashanghenzan closed 7 months ago
1
CellRanger Multi Feature Barcode Error

#237 shamer3 closed 7 months ago
1
incompatible with all the chemistries

#236 ab4cp closed 7 months ago
2
Low alignment rate when using fastq generated from bamtofastq

#235 malonzm1 closed 7 months ago
1
aligning to a multi-reference w/ ambiguities

#234 stanleyjs closed 7 months ago
1
getting more estimated number of cells

#233 archana433 closed 7 months ago
3
cellranger atac count (force cells issue)

#232 samandmac closed 7 months ago
2
What is needed from ./external/?

#231 nick-youngblut closed 7 months ago
3
cellranger 7.0.0 pipestance failed, when executing feature barcode

#230 sagrikachugh closed 7 months ago
4
spaceranger mkfastq [error] You must specify either a samplesheet or CSV file.

#229 feasiblee closed 7 months ago
1
Cellranger MkRef Error

#228 shamer3 closed 7 months ago
4
Brcode Rank Plot y-axis scale

#227 MartaBenegas closed 7 months ago
1
error in cellranger-atac mkref

#226 rahulnutron closed 7 months ago
2
Duplicate FASTQs found when use cellranger count for Feature Barcode Analysis

#225 mengchengyao closed 7 months ago
2
Cellranger-arc peak annotation error - bedtools

#224 yigitbabal closed 7 months ago
1
Using CellRanger for other UMI-based Single-Cell Platforms

#223 hkarakurt8742 closed 7 months ago
1
FASTQ file names with _001

#222 Serena-Fang closed 7 months ago
1
Bump smallvec from 0.4.1 to 1.10.0 in /lib/rust/vdj_asm

#221 dependabot[bot] closed 9 months ago
1
CellRanger-ARC for Arbidosis failed with error

#220 nilesh-iiita closed 7 months ago
9
cellranger-7.1.0: Fix cluster execution --jobmode=torque and --jobmode=pbspro

#219 mmokrejs closed 7 months ago
5
cellranger-7.1.0: patches to fix broken PYTHONPATHs

#218 mmokrejs closed 7 months ago
0
error: The subcommand 'mkref --genome=GRCh38' wasn't recognized Did you mean 'mkref'? If you believe you received this message in error, try re-running with 'cellranger -- mkref --genome=GRCh38

#217 QianRongAn closed 1 year ago
4
Bump tornado from 4.0.2 to 6.3.2 in /lib/python/fbpca

#216 dependabot[bot] closed 9 months ago
1
Bump tornado from 4.0.2 to 6.3.2 in /lib/python/fbpca/docs

#215 dependabot[bot] closed 9 months ago
1
Dehash fastq files

#214 royfrancis closed 7 months ago
1
Selecting primary alignment in duplicate reads

#213 kwcurrin closed 7 months ago
1
possorted_genome_bam.bam file not found in cellranger output folder

#212 tangybat closed 7 months ago
1
Is there a reason why cellranger multi does not support 5'-chemistry CMO libraries?

#211 dmalzl closed 7 months ago
1
cellranger multi fails on parallel file systems with shutil error

#210 dmalzl closed 1 year ago
3
Bump time from 0.1.40 to 0.2.0 in /lib/rust

#209 dependabot[bot] closed 9 months ago
1
Bump time from 0.1.38 to 0.2.0 in /lib/rust/vdj_asm

#208 dependabot[bot] closed 9 months ago
1
error while running cellranger vdj pipeline on cluster

#207 Ktek28 closed 7 months ago
2
how to solve SGE mode error

#206 felixlee0608 closed 7 months ago
1
cellranger multi only assigning one CMO

#205 cap76 closed 7 months ago
2
mkref gtf errors after v4.0.0

#204 cap76 closed 1 year ago
2
cell ranger reanalyze makes loupe file with "Invalid File Format"

#203 jeffpkamp closed 7 months ago
5
Cellranger count creating an empty matrix.mtx after adding 'N' and '#' to R1 UMI and quality respectively to account for 9bp UMI.

#202 JHorder closed 7 months ago
1
Obtain fastQ file from .bam files

#201 pmarzano97 closed 7 months ago
1
CellRanger3 vs CellRanger5 deviating results for annotation of TRA and TRB in VDJ

#200 Close-your-eyes closed 7 months ago
1
How to run cellranger on Apple M1/2 machines

#199 RenGroup closed 7 months ago
2
spaceranger mapping problem

#198 fenghuijian closed 7 months ago
1
Bump certifi from 14.05.14 to 2022.12.7 in /lib/python/fbpca

#197 dependabot[bot] closed 9 months ago
1