hzi-bifo/RiboDetector

Issues

• unexpected large proportion of rRNA reads detected by RiboDetector

  #53 opened 3 months ago by Ivy-ops
  13

• error after 14 hours of processing

  #54 opened 3 months ago by tulikasriv26
  3

• Log file/progress formatting for better readability

  #52 opened 7 months ago by mckellardw
  2

• Can we use Ribodetector for rRNA quantification in scRNASeq?

  #41 opened a year ago by Rohit-Satyam
  1

• RiboDetector for barcoded libraries

  #51 opened 8 months ago by mckellardw
  2

• Mouse data compatibility

  #50 opened 9 months ago by mmiots9
  2

• No classification at all for some data and classification for some

  #49 opened 9 months ago by EorgeKit
  6

• Classification of the rRNA removed seqeunces

  #45 opened 9 months ago by LeoVincenzi
  3

• Address already in use

  #46 opened 9 months ago by lucacozzuto
  5

• fix the issue caused by less random default socket addresses for multiprocessing.Manager()

  #47 opened 9 months ago by dawnmy
  0

• Read Length question

  #48 opened 9 months ago by singhbhavya
  1

• Ability to produce a log file that can be easily processed by MultiQC

  #33 opened a year ago by Rohit-Satyam
  18

• Tuple range error

  #44 opened a year ago by mwylerCH
  3

• Can we apply this tool for custom reference sequences?

  #43 opened a year ago by ssun1116
  2

• RuntimeError: indices should be either on cpu or on the same device as the indexed tensor (cpu)

  #40 opened a year ago by caldodge
  9

• ValueError:you are required to explicitly set the providers parameter when instantiating InferenceSession

  #42 opened a year ago by Abelcanc3rhack3r
  1

• Change the log info, from detect_cpu to ribodetector_cpu

  #35 opened a year ago by dawnmy
  0

• [ERROR] Unable to run ribodetector on a remote server: No visible CUDA devices!

  #36 opened a year ago by jwilliams648
  1

• RiboDetector is identifying reads generated from ChrX and ChrY as rRNA reads

  #37 opened a year ago by rajanbit
  4

• The proportion of ribosome reads calculated by ribodetector is not equal to the proportion of ribosome protein count in ReadsPerGene.out.tab generated by STAR

  #39 opened a year ago by li1311139481
  2

• Retrive the filtered out sequences

  #38 opened a year ago by LeoVincenzi
  2

• ribodetector_cpu hangs with SLURM

  #31 opened a year ago by gianfilippo
  4

• RiboDetector is not working on GPU mode

  #34 opened 2 years ago by Nirmal2310
  4

• Please use detect_cpu.py to run it on CPU if you do not have GPU or you need to install GPU version of PyTorch

  #32 opened 2 years ago by Rohit-Satyam
  2

• Recommendations on running RiboDetector twice on the fastq files?

  #30 opened 2 years ago by resol341
  2

• ribodetector_cpu classifies and outputs more reads in the end than there were in the input data to begin with

  #29 opened 2 years ago by erzakiev
  13

• Which organism?

  #28 opened 2 years ago by Homap
  1

• no rRNA sequences were detected in an almost complete genome

  #11 opened 3 years ago by ThomasYJK555
  2

• Chunk size question

  #27 opened 2 years ago by caity-s
  3

• gzip is very slow

  #26 opened 2 years ago by alienzj
  1

• Question

  #25 opened 2 years ago by deoliveira86
  2

• docker image for 0.2.6

  #22 opened 2 years ago by NicoleGruenheit
  3

• question regarding confidence of -e norrna option

  #23 opened 2 years ago by caity-s
  4

• CPU mode hangs with macOS

  #18 opened 2 years ago by omicz
  6

• Using RiboDetector on assembled contigs?

  #24 opened 2 years ago by natashagriffin
  2

• Add model eval?

  #14 opened 2 years ago by dawnmy
  1

• read length should be not smaller than 50, but ribo-seq reads are ~30 bp

  #16 opened 2 years ago by huguanjing
  4

• False postivies when using on metagenomic data?

  #21 opened 2 years ago by rezenman
  6

• cpu vs. gpu performance

  #17 opened 2 years ago by ARW-UBT
  4

• About read length

  #20 opened 2 years ago by gouwei1
  2

• Is it possible using Ribodector on metagenomic reads

  #19 opened 2 years ago by lideyongJNU
  1

• Installation error in conda environemnt

  #15 opened 3 years ago by ARW-UBT
  6

• Memory Calculation Doubts

  #12 opened 3 years ago by magcurly
  7

• Memory issues with RiboDetector

  #9 opened 3 years ago by akrinos
  23

• Add chunk size support for loading the sequences to reduce memory use for large files

  #10 opened 3 years ago by dawnmy
  2

• In CPU mode, smaller chunk_size does not reduce the memory use.

  #13 opened 3 years ago by dawnmy
  3

• Process hangs in CPU detection step

  #6 opened 3 years ago by sjaenick
  23

• GPU with higher CUDA version can not be used within old pytorch

  #8 opened 3 years ago by sixvable
  12

• Optimize for CPU which supports AVX2 instruction

  #5 opened 3 years ago by dawnmy
  0

• Lost reads?

  #7 opened 3 years ago by sjaenick
  2