nanocompore

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Downsample to the same coverage as the lower coverage sample

2

Very different coverage between samples might causes troubles during GMM clustering. At the moment we can downsample to a fixed coverage level, but it would be great to downsample each...

tleonardi

**Describe the bug** Dear Nanocomopore team (@lmulroney), Thank you for this very useful software. This is not an issue rather help is needed to run the nanocompore's sampcomp. **My script...

rezarahman12

**Script for generating the "Sharkfin plot (Figure 4A) of the p-values compared with Log Odds Ratio"** Thank you very much for developing and publishing the nanocompore pipeline and its python...

sbridgett

The result tsv file I run from SampComp is like this, pos chr genomicPos ref_id strand ref_kmer GMM_logit_pvalue KS_dwell_pvalue KS_intensity_pvalue GMM_cov_type GMM_n_clust cluster_counts Logit_LOR 10 NA NA NC_004162.2 NA AGACA...

JeremyQuo

ref kmer and position of modification

3

If a significant change in methylation is detected, at which base pair is this change? Is it the position indicated by the pos column or perhaps the middle of the...

keenhl

Direction of change in methylation

1

If a significant change in methylation is determined at a particular position, how can one determine the direction of change. In other words, is there any way to determine if...

keenhl

sharkfin plot too many data points and difficult to visualize

1

Hi, I was trying to make the sharkfin plot as you discussed in another [issue](https://github.com/tleonardi/nanocompore/issues/206). However, the shape of my plot doesn't match the shape you showed in the paper...

Rohit-Satyam

updated jsmin to 3.0.1 in poetry.lock file to fix github installation failures updated patsy to 0.5.6 in poetry.lock file to fix depreciation warning changed all instances of np.float to np.float64...

lmulroney

db type is dbm.gnu, but the module is not available

4

Hello, I am following your instructions and I get this error: 2023-11-15 15:55:54.103 | INFO | nanocompore.SampCompDB:__init__:55 - Loading SampCompDB 2023-11-15 15:55:54.108 | ERROR | nanocompore.common:__init__:22 - The result database...

villegmb

Nanocompore SampComp stuck at 0%

8

**Describe the bug** Hi, I've been trying to run SampComp on 6 samples of ONT Direct RNA-seq on a METTL3 KD cell line for some time, and have yet to...

sidizhao