tombo

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Tombo detect modifications de novo with corrected reads and reproducibility

2

Hello, I’m using Tombo to detect modifications ‘de novo’ on direct RNA data. I’m using the following commands (as described in MINES pipeline since the idea is to use MINES...

FraPria

text output

3

Hi, dear developer! When I ran "tombo detect_modifications model_sample_compare" and "tombo text_output browser_files", I met a question. My commands are as follows: tombo detect_modifications model_sample_compare --fast5-basedirs ./treatment-fast5/ --control-fast5-basedirs ./control-fast5/ --statistics-file-basename...

AicuiZhang

Hi Marcus, I wanted to suggest additions to the documentation on these pages: * https://nanoporetech.github.io/tombo/modified_base_detection.html#tombo-statistics-file-format * https://nanoporetech.github.io/tombo/text_output.html * https://nanoporetech.github.io/tombo/tombo.html As written, it's not clear that functions like ``get_pos_stat`` in the...

SycamoreLeaf

Documentation for tombo build_model estimate_alt_reference could be clearer

1

Hello, I have been trying to train an alternative model to get more accurate RNA mod detection at higher modification densities, and was trying to run `tombo build_model estimate_alt_reference ...`...

patbohn

Alignments visualization

1

Hi all and thanks for your work. According to the documentation, "The first step in any Tombo analysis is to re-squiggle (raw signal to reference sequence alignment) raw nanopore reads....

fanavarro

Can I see Tombo Index File

1

I want to extract the current signal when a base pass through the nanopore. i.e. the current signal value for each position on the read. It seems that this information...

yuxinPenny

Tombo API, read statistic file

7

Hello I am using the level_sample_compare method to identify differentially modified sites between samples of direct RNA: `tombo detect_modifications level_sample_compare --fast5-basedirs RNA_M2/single_fast5 --alternate-fast5-basedirs RNA_M1/single_fast5 --processes 10 --statistics-file-basename sample.compareM1C_M2` When I...

ceslobfer

[Bug?] Resquiggle error after shuffle fastq order

3

Hi , I want to resquiggle part of fastq records (because too many of them). I shuffle fastq record first (to make sure sample evenly) and sample a potion from...

yipukangda

Resquiggle process stuck at 0

13

I came across a problem when using tombo command lines. The tombo resquiggle started and ran normally but the progree bar just stuck at 0 and no content was written...

orangehe

Error while using --overplot Boxplot

1

Hi, I encountered an error while running tombo plot with --overplot Boxplot. Other plotting commands worked perfectly fine. I passed this command: tombo plot most_significant --fast5-basedirs /my/fast5/dir --control-fast5-basedirs /my/control/fast5/dir --statistics-filename...

nemitheasura