eesiribloom

Sniffles2 missing high confidence deletions with sufficient read support and depth of coverage

1

I have a set of high-confidence consensus SVs called from illumina WGS data which I want to compare to SVs called with nanopore long-reads. There seems to be a surprisingly...

cycle view

1

If I have files output from AA and AC, is there a way for me to experiment with the cycle view /genome browser to investigate potential larger structures formed from...

basecalling with hac v4.2 vs v4.3 model

1

If I have two "batches" of sequencing data and one is basecalled with: [email protected] and the other with: [email protected] Will this greatly affect my results? Should re-do basecalling so all...

If I want to detect somatic SVs with matched tumor and normal data by subtracting SVs present in both normal and tumour, should i use `--tumor` with the tumor data...

training more models

2

I would like to try using ClairS-TO with my data but there isn't the right models available. Are any of these likely to become available any time soon? dna_r10.4.1_e8.2_400bps_hac (5khz)...

Difference in total counts of each probability per modification in different pore chemistries

5

I have samples basecalled with dorado software (v0.4.1) with detection of 5mCG_5hmCG modifications enabled using either: [email protected] [email protected] I've noticed the two "batches" have distinct distribution of probabilities in base...

using SNV/SNP file with spectre in tumour samples

3

I am calling CNVs in tumour ONT long-reads and want to try using spectre I assume it is preferred to input SNPs from a matched tumour sample rather than germline...

Which model should I use for R9.4.1 data basecalled with dorado

1

I have R9.4.1 data basecalled with dorado (HAC). What is the most suitable model to use?

modkit summary shows unexpected proportion of methylation - is my methylation information being lost

4

When I run modkit summary on my samples I am getting a strange batch effect. I have two batches of samples: 1st batch re-basecalled with dorado standalone software **v0.6.1** model...

Is there a way to calculate DMRs from WGBS control data/ bigwig input

1

I want to calculate DMRs using a reference sample provided by a cell-type specific [atlas](https://www.nature.com/articles/s41586-022-05580-6#data-availability) of methylation as I do not have a matched normal bam. Is there a way...