f5c

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Empty bam and tsv file with f5c methylation calling

3

Hi, I am trying to use f5c and follow the "[Resource efficient methylation calling workflow for a dataset with many ultra-long reads](https://hasindu2008.github.io/f5c/docs/example-usage#resource-efficient-methylation-calling-workflow-for-a-dataset-with-many-ultra-long-reads). However, the methylation call failed and I think...

PanZiwei

few sites from LSK114

3

Hi, I'm using f5c to call methylation sites from LSK114. I'm obtaining only few sites. Is f5c ready to be used on LSK114? How should I implement f5c on reads...

ogrecio

Error in eventalign

5

Well, I test f5c to index, it really faster than before. It works! but when I use f5c to eventalign, it print out on screen: [E::faidx_adjust_position] The sequence "NM_001035539.1" not...

Tomcxf

[Request] An option to filter out signal spikes

5

Hi Hasindu, thank you for developing f5c and the detailed documentation with it, it is incredibly fast. I am using it to detect RNA modifications, and in one part of...

patbohn

avoid skip when using f5c eventalign

8

Hi f5C team! I wonder if there are any settings to avoid event skip when using f5c eventalign? I found not all bases in reference would have event in f5c...

xieyy46

When doing f5c call-methylation, the quality of dorado basecaller's reads was significantly lower than that of guppy basecaller's reads

4

This is the full log of the f5c call-methylation:  This is dorado basecaller's order： dorado basecaller /share/home/yzwl_hanxs/app/dorado-0.5.3-linux-x64/model/[email protected] ./pod5/ | amtools view -bhS -@ 10 > test.bam Convert bam to...

happier21

Difference between f5c eventalign and resquiggle, event segmentation with resquiggle

4

Hello, I am wondering about the difference between `eventalign` and `resquiggle`. As I understand it from https://hasindu2008.github.io/f5c/docs/output, `resquiggle` aligns a nucleotide sequence to a raw signal (without needing alignment to...

maximilianmordig

Bad fast5 warning . How to I fix ? code I run and output attached ( r10 chemistry)

1

f5c call-methylation -t 8 -r BC9to16.fastq -b BC9to16decomfast5.sorted.bam -g cdiffstr22457.fasta > BC9to16b.tsv [meth_main::INFO] Default methylation tsv output format is changed from f5c v0.7 onwards to match latest nanopolish output. Set...

senukobla

Default parameters used in Event detection function

8

Hi there, I have some questions about the event detection, which I knew was adopted from nanopolish/scrappie. I found the default parameters were different between RNA and DNA event detection....

loganylchen

recommended threshold for the log likelihood ratio

4

Hi @hasindu2008 and all, For the `f5c meth-freq` step, is the reommended threshold for the log likelihood ratio still 2.5, or should be 2.0 as nanopolish has changed? Thank you...

PengNi