nanoporetech / tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

nanoporetech/tombo Issues

Cannot annotate fast5
Closed 10 days ago1
Which strand to use in RNA modification?
Updated a month ago
Support RNA004 kit in Tombo
Updated a month ago3
none correlation between modification position and +/- 1
Updated 2 months ago2
Can't install Tombo under current Ubuntu installation
Updated 2 months ago2
Tombo installation issue with bioconda
Closed 2 months ago3
Fail to Install tombo using venv3 Ubuntu18.04
Updated 2 months ago1
Cannot install on Mac OS
Updated 2 months ago1
overplot-type doesn't work
Updated 2 months ago1
Problem importing Tombo in python
Updated 2 months ago1
tombo resquiggle 0%|
Updated 6 months ago2
Resquiggle Process stuck at 0
Closed 9 months ago4
[resquiggle] Most of my reads are unsuccessful bc "extends beyond bandwidth"
Updated 6 months ago2
Slow Re-squiggle though set --process 40 to run tombo resquiggle over multiple cores
Updated 6 months ago3
Tombo preprocess error
Closed 6 months ago4
issue when running re-squiggle
Updated 6 months ago2
Will this affect my next analysis
Updated 6 months ago2
Endless running Tombo resuiggle, reached to 100% in resuiggle but doesn't finish the job
Updated 6 months ago1
Unsuccessful resquiggle for RNA
Updated 6 months ago4
ERROR: 'utf-8' codec can't decode byte 0x8b
Updated 7 months ago4
preprocessing for tombo
Updated 8 months ago2
preprocessing for tombo
Closed a year ago2
Unable to install ont-tombo via condo and pip
Closed 9 months ago4
tombo plot error: Encountered invalid genome sequence request
Updated 9 months ago
call methylation site
Closed 9 months ago2
FloatingPointError: invalid value encountered in true_divide
Closed 9 months ago1
Model sample compare with different lengths of DNA
Closed 9 months ago1
Tombo for RNA modification prediction using direct RNA sequencing
Closed 9 months ago1
Endless running Tombo resuiggle, reached to 100% in resuiggle but doesn't go to next step, generate output files
Updated 9 months ago1
tombo preprocess can not attach basecall information
Closed 2 years ago3
tombo preprocess annotate_raw_with_fastqs
Updated a year ago16
Trouble with Tombo pipeline for RNA-Direct Sequencing
Updated a year ago1
tombo installing error by pip
Updated a year ago1
too slow in step tombo resquiggle:Getting file list with more than 9000kb reads
Closed a year ago1
How is expected fraction abundance calculated? Does it normalize for coverage in treated vs untreated conditions?
Updated a year ago
Instalation issue with python 3.9 and last version of conda
Updated a year ago1
Is there a minimum sequence length/ can resquiggle work with a 38 nt reference?
Updated a year ago
Problems in starting the analysis. Please help me
Updated a year ago1
Trimming raw signal based on genomic location
Updated a year ago1
de novo & meme
Updated a year ago
No basecalls found during resquiggle on RNA fast5s
Updated a year ago7
difficult installing tombo on mac os Monterey; python version important
Updated a year ago2
Error with tombo preprocess
Updated a year ago2
Preprocess annotate_raw_with_fastqs halting issue
Updated 2 years ago
Error while reading Statistic File
Updated 2 years ago
tombo build_model estimate_reference global name 'motif' is not defined
Updated 2 years ago
Different output in wig file in every running
Closed 2 years ago1
How can I get this folder "test_data" ? I want to run tombo/tombo/tests/shell_tests.sh.
Closed 2 years ago
Raising an error and exit with the tombo_helper function should return non-zero value
Updated 2 years ago
Different versions of guppy have an impact on tombo?
Updated 2 years ago