velocyto-team velocyto.py issues

velocyto-team / velocyto.py

RNA velocity estimation in Python

http://velocyto.org/velocyto.py/

BSD 2-Clause "Simplified" License

160 stars 83 forks source link

issues

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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!

#358 AsyaTiho opened 1 year ago
2
gene name issue

#357 YichaoOU closed 1 year ago
1
CellRanger --include-introns

#356 GEmilioHO opened 1 year ago
0
Memory

#355 milescsmith closed 1 year ago
0
memory samtools problems in velocyto run

#354 ElenaSLuis opened 1 year ago
1
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb2 in position 0: invalid start byte

#353 nroak opened 1 year ago
0
Fresh Installation is not working

#352 adRn-s opened 1 year ago
1
Failed to install velocyto on macOS

#351 r-osorio opened 1 year ago
4
Killed after "generating data table" message

#350 yuyuliu closed 1 year ago
3
running run-dropest

#349 bxxu opened 1 year ago
4
velocyto on non-UMI bam -U flag

#348 anafilia opened 2 years ago
2
velociyto memory issues

#347 rimmoussa opened 2 years ago
0
Deal with BD Rhapsody out file

#346 x1han opened 2 years ago
5
What command is used to remove reads fully overlapping repeats?

#345 apredeus opened 2 years ago
0
Error in SAMPLEFOLDER

#344 skoturan opened 2 years ago
12
Problem with velocyto run with inDrops data

#343 smanessi opened 2 years ago
0
Strange spliced/unspliced percentages with cell hashed data

#342 carbycrab opened 2 years ago
1
Bam file : No EOF marker; file may be truncated

#341 GouQiao opened 2 years ago
0
Velocyto samtools memory error

#340 pbpayal opened 2 years ago
1
Fail to install velocyto

#339 FionaMoon opened 2 years ago
1
Killed no matter how large the memory is

#338 diyang1354 opened 2 years ago
0
mac m1 velocyto error

#337 parkjooyoung99 opened 2 years ago
6
How to run10x on multiple folders in one command?

#336 Dragonmasterx87 closed 1 year ago
0
Failed to install velocyto.py in Mac - clang: error: unsupported option '-fopenmp'

#335 parkjooyoung99 opened 2 years ago
2
Does a low `unspliced` proportion have an impact on velocity calculation ?

#334 jiangpuxuan opened 2 years ago
1
Make run10x faster

#333 michaeleekk opened 2 years ago
1
run10x with custom reference that is in gtf.gz format

#332 michaeleekk opened 2 years ago
0
velocyte `run10x` error: Genome annotation gtf file is not sorted correctly!

#331 jiangpuxuan opened 2 years ago
2
velocyto run remains hanging at the end when executing on SLURM

#330 edg1983 opened 2 years ago
0
Unable to load the content of the .loom file into an interactive session of python

#329 shikhagupta68 opened 2 years ago
0
GTF: AttributeError: 'NoneType' object has no attribute 'group'

#328 bbimber opened 2 years ago
6
Pysam not found even after installing velocyto

#327 dajsfiles closed 4 months ago
0
ERROR - Can not locate the barcodes.tsv file! using cellranger multiplexing (cellranger v6.1)

#326 bsmith030465 opened 2 years ago
3
Issue with BAM file and velocyto

#325 abuchin opened 2 years ago
1
Velocyto Error

#324 raha-nasrabadi opened 2 years ago
0
ERROR - Can not locate the barcodes.tsv file! for Cellranger Multiplexing outputs

#323 danli349 opened 2 years ago
5
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa7 in position 0: invalid start byte

#322 vagabond12 opened 2 years ago
6
Could not find index file but still generated the loom from bam -- run10x error?

#321 denvercal1234GitHub opened 2 years ago
8
How to fix MemoryError (f" bam file #{k} could not be sorted by cells. \n\ in run10x and run?

#320 denvercal1234GitHub closed 2 years ago
14
Is it the right genome annotation file for cellranger 10X human to use? Chromosome MT+/- and others not present in the annotation

#319 denvercal1234GitHub closed 2 years ago
4
no mitochondrial genes are included in loom file (bug fixed, velocyto team please check this)

#318 hyjforesight closed 2 years ago
19
Error while running velocyto run10x

#317 yurasong opened 3 years ago
3
velocyto run OSError: no BGZF EOF marker; file may be truncated

#316 shijianasdf opened 3 years ago
4
Invalid value for 'GTFFILE'

#315 linscnano opened 3 years ago
1
Memory issues when using run10x

#314 leahrosen closed 3 years ago
1
BlockingIOError: [Errno 11] Unable to open file (unable to lock file, errno = 11, error message = 'Resource temporarily unavailable')

#313 varunkas opened 3 years ago
1
Adding metadata to my Velocyto run

#312 AAA-3 closed 3 years ago
1
UMI Barcode Entry and Samtools error on 10X Cell Ranger GTF and BAM files

#311 AAA-3 closed 3 years ago
11
Velocyto run10x Syntax Error

#310 AAA-3 closed 3 years ago
7
pip install error

#309 zhenzuo2 opened 3 years ago
0

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