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DNA vs RNA from raw reads

1

Hi there, I don't have an issue as such, more a (hopefully) quick question about how Tombo determines whether a sample is DNA or RNA from the raw reads in...

Alannahh

Different number of normalised and raw signals

2

Hello, I am new with Tombo and I have processes the same file with both Python API and commands, however, when I load the raw signal from the fast5, I...

mrubio-chavarria

Hi: I got an error in a file named unexpected_tombo_errors.1252.err when I run the direct-RNA resquiggle. The command and error are as follows: `tombo resquiggle ${sigle_fast5_dir} ${transcriptome} --processes 10 --num-most-common-errors...

RainaYin-sys

about tombo resquiggle

2

Hi！as we know that the current of RNA sample in the nanopore is determined by 5 continuous bases, however, in tombo resquiggle result event table (as showed below), one event...

xieyy46

.tombo.index file ReadData object order is different than in documentation

2

Hello, I wanted to investigate the signal-matching-scores of my reads after resquiggling, and if I understand correctly this is most straightforward by looking into the tombo.index files (see quote below)....

patbohn

ValueError: need at least one array to concatenate

1

Hi,teacher!When i run 'tombo detect_modifications level_sample_compare' i meet another problem.Can you give me some advice ?Thank you very much ! 

Bessyyi

How could i analaysis cp_alt_6mA_model.difference.minus.wig

1

Hello,dear teacher! I run the command "tombo detect_modifications alternative_model --fast5-basedirs /home/ywj/fang_lab/NAT_single_fast5/ --alternate-fast5-basedirs /home/ywj/fang_lab/WGA_single_fast5/ --alternate-bases 6mA --statistics-file-basename CP.level_compare_6mA_sample" and "tombo text_output browser_files --fast5-basedirs /home/ywj/fang_lab/NAT_single_fast5 --statistics-filename /home/ywj/tombo/output/CP.level_compare_6mA_sample.6mA.tombo.stats --browser-file-basename cp_alt_6mA_all_model --file-types dampened_fraction".Then i...

Bessyyi

Does Tombo plot kmer for RNA use reverse complement kmers?

1

Hi, I want to plot kmer values of direct RNA sequenced samples, and got it to work successfully, but it appears that C and U center bases have the lowest...

patbohn

Hello! We all know that nanopore detects the current which is composed of 5 bases of RNA. So i want to know what the base in this table(fast5file/Analyses/RawGenomeCorrected_000/BaseCalled_template/Events) which is...

zhongzhendong

fasta file upload error

5

I tried several commands after the reference file path in the resquiggle command but every time it is showing the following error.  However the minimap2 is working fine. I...

AnunayS