-
For duplex basecalling of barcoded data I'm looping over the barcode directories to find the reads in the simplex fastqs. Then I duplex basecall these with the following command:
`/home/vc/ont/dora…
-
Hello, we are running dorado on 2 samples. One native DNA vs the PCR amplified one that "in theory" should not hold the methylation.
Why do we get a methylation signal in the PCR sample?
The methyl…
BioRB updated
4 months ago
-
-
Hello MerenLab,
While at EBAME I was encouraged to open this discussion by @FlorianTrigodet and @ivagljiva, and bring it to @semiller10's attention.
DNA methylation is on the verge of constituti…
-
https://gdc.cancer.gov/about-data/gdc-data-processing
-
Hi,
I am trying to run reptile on pre-trained model mm_model_coreMarks.reptile using methylation data. Is there any issue with bw generation, I have methylation base call bed files containing chr no,…
-
Hi there,
We are working on longitudinal data from DNA methylation, and I know ImpulseDE2 deals great with time course data for RNAseq datasets and its hypothesis is on a NB distribution for gene cou…
-
```
5mC and 5hmC are common DNA methylations. Single-base methylation seq data are
quite different from histone modification ChIP-seq data in the way of how the
methylation information is encoded in…
-
Hi,
I've run `modkit summary` on some modified bam files (5mC and 5hmC calling). Base calling was done using Dorado 0.7.0 using model dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1. I've used `modk…
-
Hi Dr. Wang,
I have just read your paper "A mouse model with high clonal barcode diversity for joint lineage,
transcriptomic, and epigenomic profifiling in single cells" and fairly interested in the…