velocyto-team/velocyto.py issues and pull requests

#404 - Unable to retrieve spliced/unspliced RNA from single nuclei isolation

Issue - State: open - Opened by hyjforesight 15 days ago

#403 - Integrating Ambient RNA Removal (CellBender) into Velocity Analysis

Issue - State: open - Opened by Evenlyeven about 1 month ago

#402 - Merging multiple loom files with different reference genome

Issue - State: open - Opened by yechanYS about 2 months ago

#401 - Retriving genes with caracterisitic velocity behavior accorindg to latent time

Issue - State: open - Opened by Dalhte 2 months ago

#400 - When calculate the unspliced reads, does UTR region included or not?

Issue - State: open - Opened by DieTANG 2 months ago

#399 - Memory & run time issue run10x

Issue - State: closed - Opened by DelongZHOU 3 months ago - 1 comment

#398 - Velocyto ran successfully but main matrix is missing

Issue - State: closed - Opened by econnolly7 3 months ago - 2 comments

#397 - Package dependency problem on NumPy

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

#396 - How to get fastq header information of spliced and unspliced 10X short reads

Issue - State: open - Opened by wenhu0701 3 months ago

#395 - Incorrect trimming of chromosome name leads to IOError(f"Input .bam file should be chromosome-sorted. (Hint: use `samtools sort {bamfile}`)")

Issue - State: open - Opened by kepbod 3 months ago - 3 comments

#394 - Mark spliced/unspliced reads on original BAM file

Issue - State: open - Opened by taffy-miao 4 months ago

#393 - Seems like a typo.

Issue - State: open - Opened by chenqiuhao 4 months ago

#392 - Additional gene problem

Issue - State: open - Opened by Cadaqoes 5 months ago

#391 - Using spatial transcriptomics data on Velocyto.py generates lower counts than Space Ranger

Issue - State: open - Opened by biyang-bioinfo 5 months ago

#390 - Inquiry on the input for running "velocyto run10x"

Issue - State: open - Opened by daisyko 5 months ago

#389 - velocyto on filtered or raw matrix or from matrix corrected ?

Issue - State: open - Opened by Sirin24 6 months ago

#388 - WARNING - The .bam file refers to a chromosome not present in the annotation (.gtf) file

Issue - State: open - Opened by sekekeretsu 7 months ago - 4 comments

#387 - OSError: truncated file is occured in cellranger-5.0.1-dirty output.

Issue - State: open - Opened by ilovegreentea 7 months ago

#386 - index file

Issue - State: open - Opened by sherinesaber 9 months ago - 1 comment

#385 - how do i generate the repeat sequences masked gtf file from Ensembl?

Issue - State: open - Opened by erzakiev 9 months ago

#384 - When and when not to use "repeat annotation mask" in 10X?

Issue - State: open - Opened by denvercal1234GitHub 9 months ago

#383 - Question about latent parameter t

Issue - State: open - Opened by taffy-miao 10 months ago

#382 - BlockingIOError: [Errno 35] 'Resource temporarily unavailable' on Mac OS X

Issue - State: open - Opened by YitengDang 10 months ago

#381 - [E::bgzf_read_block] Failed to read BGZF header at offset X

Issue - State: closed - Opened by YitengDang 10 months ago - 1 comment

#380 - Unable to run velocyto: samtools issue

Issue - State: open - Opened by millerkaplanlab 11 months ago - 1 comment

#379 - TypeError: create() got an unexpected keyword argument 'matrix'

Issue - State: open - Opened by zcaiwei 11 months ago

#378 - Passing velocyto samtools memory for sorting step

Issue - State: open - Opened by wudustan 11 months ago

#377 - ImportError: speedboosted.cpython-38-x86_64-linux-gnu.so: undefined symbol: __log10_finite

Issue - State: open - Opened by lili03080317 11 months ago - 3 comments

#376 - Get tons of warnings when running

Issue - State: open - Opened by dingyaozhang 12 months ago - 1 comment

#375 - Batch effects in combining multiple loom files

Issue - State: open - Opened by anshu957 12 months ago - 2 comments

#374 - ValueError: Column attribute 'Clusters' is not the same length (0) as number of columns in main matrix (3708)

Issue - State: open - Opened by denvercal1234GitHub about 1 year ago

#373 - Error in run10X: logging.debug(f"Example of barcode: {valid_bcs_list[0].split('-')[0]} and cell_id: {valid_cellid_list[0]}") - IndexError: list index out of range

Issue - State: open - Opened by denvercal1234GitHub about 1 year ago - 1 comment

#372 - AttributeError: 'NoneType' object has no attribute 'group'

Issue - State: open - Opened by danli349 about 1 year ago

#371 - Running velocyto on 10x Cell Ranger cloud-generated files

Issue - State: closed - Opened by schroeme about 1 year ago - 4 comments

#370 - Testing

Pull Request - State: closed - Opened by milescsmith about 1 year ago

#369 - Compatibility with non-string form for barcodes and UMIs

Issue - State: open - Opened by weir12 over 1 year ago

#368 - Multi-omic

Issue - State: open - Opened by zhangqc723 over 1 year ago

#367 - velocyto Index Out of Range

Issue - State: open - Opened by TamaraSall over 1 year ago - 2 comments

#366 - Issues running velocyto

Issue - State: open - Opened by Battamama over 1 year ago - 1 comment

#365 - Unexpected MemoryError: bam file #0 could not be sorted by cells.

Issue - State: open - Opened by monica-nicolau over 1 year ago

#364 - High % of unspliced from 10X scRNAseq in tissues

Issue - State: open - Opened by denvercal1234GitHub over 1 year ago - 5 comments

#363 - Do not resolve paths for bamfile and barcodes:

Pull Request - State: open - Opened by tucano over 1 year ago

#362 - how velocyto fits to cellrange-arc output

Issue - State: open - Opened by zqmiao-mzq over 1 year ago - 2 comments

#361 - meanings of layers

Issue - State: open - Opened by songmingl over 1 year ago - 2 comments

#360 - possorted_genome_bam.bam file not found in cellranger output folder

Issue - State: open - Opened by tangybat over 1 year ago - 1 comment

#359 - Error when running velocyto run-smartseq2

Issue - State: open - Opened by ETAOIK over 1 year ago - 1 comment

#358 - ERRORS when running velocyto: ERROR - This is an older version of cellranger, cannot check if the output are ready, make sure of this yourself! ERROR - Can not locate the barcodes.tsv file!

Issue - State: open - Opened by AsyaTiho over 1 year ago - 2 comments

#357 - gene name issue

Issue - State: closed - Opened by YichaoOU over 1 year ago - 1 comment

#356 - CellRanger --include-introns

Issue - State: open - Opened by GEmilioHO over 1 year ago

#355 - Memory

Pull Request - State: closed - Opened by milescsmith over 1 year ago

#354 - memory samtools problems in velocyto run

Issue - State: open - Opened by ElenaSLuis over 1 year ago - 1 comment

#353 - UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb2 in position 0: invalid start byte

Issue - State: open - Opened by nroak over 1 year ago

#352 - Fresh Installation is not working

Issue - State: open - Opened by adRn-s over 1 year ago - 1 comment

#351 - Failed to install velocyto on macOS

Issue - State: open - Opened by r-osorio over 1 year ago - 4 comments

#350 - Killed after "generating data table" message

Issue - State: closed - Opened by yuyuliu over 1 year ago - 3 comments

#349 - running run-dropest

Issue - State: open - Opened by bxxu almost 2 years ago - 4 comments

#348 - velocyto on non-UMI bam -U flag

Issue - State: open - Opened by anafilia almost 2 years ago - 2 comments

#347 - velociyto memory issues

Issue - State: open - Opened by rimmoussa almost 2 years ago

#346 - Deal with BD Rhapsody out file

Issue - State: open - Opened by x1han about 2 years ago - 4 comments

#345 - What command is used to remove reads fully overlapping repeats?

Issue - State: open - Opened by apredeus about 2 years ago

#344 - Error in SAMPLEFOLDER

Issue - State: open - Opened by skoturan about 2 years ago - 12 comments

#343 - Problem with velocyto run with inDrops data

Issue - State: open - Opened by smanessi about 2 years ago

#342 - Strange spliced/unspliced percentages with cell hashed data

Issue - State: open - Opened by carbycrab about 2 years ago - 1 comment

#341 - Bam file : No EOF marker; file may be truncated

Issue - State: open - Opened by GouQiao about 2 years ago

#340 - Velocyto samtools memory error

Issue - State: open - Opened by pbpayal over 2 years ago - 1 comment

#339 - Fail to install velocyto

Issue - State: open - Opened by FionaMoon over 2 years ago - 1 comment

#338 - Killed no matter how large the memory is

Issue - State: open - Opened by diyang1354 over 2 years ago

#337 - mac m1 velocyto error

Issue - State: open - Opened by parkjooyoung99 over 2 years ago - 6 comments

#336 - How to run10x on multiple folders in one command?

Issue - State: closed - Opened by Dragonmasterx87 over 2 years ago

#335 - Failed to install velocyto.py in Mac - clang: error: unsupported option '-fopenmp'

Issue - State: open - Opened by parkjooyoung99 over 2 years ago - 2 comments

#334 - Does a low `unspliced` proportion have an impact on velocity calculation ?

Issue - State: open - Opened by jiangpuxuan over 2 years ago - 1 comment

#333 - Make run10x faster

Issue - State: open - Opened by michaeleekk over 2 years ago - 1 comment

#332 - run10x with custom reference that is in gtf.gz format

Issue - State: open - Opened by michaeleekk over 2 years ago

#331 - velocyte `run10x` error: Genome annotation gtf file is not sorted correctly!

Issue - State: open - Opened by jiangpuxuan over 2 years ago - 2 comments

#330 - velocyto run remains hanging at the end when executing on SLURM

Issue - State: open - Opened by edg1983 over 2 years ago

#329 - Unable to load the content of the .loom file into an interactive session of python

Issue - State: open - Opened by shikhagupta68 over 2 years ago

#328 - GTF: AttributeError: 'NoneType' object has no attribute 'group'

Issue - State: open - Opened by bbimber over 2 years ago - 6 comments

#327 - Pysam not found even after installing velocyto

Issue - State: closed - Opened by dajsfiles over 2 years ago

#326 - ERROR - Can not locate the barcodes.tsv file! using cellranger multiplexing (cellranger v6.1)

Issue - State: open - Opened by bsmith030465 over 2 years ago - 3 comments

#325 - Issue with BAM file and velocyto

Issue - State: open - Opened by abuchin over 2 years ago - 1 comment

#324 - Velocyto Error

Issue - State: open - Opened by raha-nasrabadi over 2 years ago

#323 - ERROR - Can not locate the barcodes.tsv file! for Cellranger Multiplexing outputs

Issue - State: open - Opened by danli349 almost 3 years ago - 5 comments

#322 - UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa7 in position 0: invalid start byte

Issue - State: open - Opened by vagabond12 almost 3 years ago - 6 comments

#321 - Could not find index file but still generated the loom from bam -- run10x error?

Issue - State: open - Opened by denvercal1234GitHub almost 3 years ago - 8 comments

#320 - How to fix MemoryError (f" bam file #{k} could not be sorted by cells. \n\ in run10x and run?

Issue - State: closed - Opened by denvercal1234GitHub almost 3 years ago - 14 comments

#319 - Is it the right genome annotation file for cellranger 10X human to use? Chromosome MT+/- and others not present in the annotation

Issue - State: closed - Opened by denvercal1234GitHub almost 3 years ago - 4 comments

#318 - no mitochondrial genes are included in loom file (bug fixed, velocyto team please check this)

Issue - State: closed - Opened by hyjforesight almost 3 years ago - 19 comments

#317 - Error while running velocyto run10x

Issue - State: open - Opened by yurasong almost 3 years ago - 3 comments

#316 - velocyto run OSError: no BGZF EOF marker; file may be truncated

Issue - State: open - Opened by shijianasdf almost 3 years ago - 4 comments

#311 - UMI Barcode Entry and Samtools error on 10X Cell Ranger GTF and BAM files

Issue - State: closed - Opened by AAA-3 about 3 years ago - 11 comments

#308 - Genes have lower counts in velocyto

Issue - State: open - Opened by jinyoung5484 over 3 years ago - 1 comment

GitHub / velocyto-team/velocyto.py issues and pull requests