remora

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Regarding m6A modified basecalling

5

Hi, I was trying to do m6A modified basecalling of data generated from R9 flowcell by using trained RNN model i.e. res_dna_r941_min_modbases-all-context_v001 by using guppy v3.5.1. But, unfortunately, I was...

PRIYANKA-22091995

NotImplementedError() when finetuning remora model

1

Hello, I am trying to finetune this model to call 6mA (`dna_r10.4.1_e8.2_5khz_400bps_sup_v4.2.0_6ma_v2.pt`), but independently from how many layers I try to freeze (I've also tried with 0) I run into...

palakela

Support for Standalone 5mC and/or 5mCG in dorado Basecalling Model Version 4.3.0

1

Hello everyone, as of dorado basecalling model version 4.3.0, only 5mC_5hmC or 5mCG_5hmCG modified bases are supported, not 5mC or 5mCG alone. This leads to problems in the downstream analysis,...

wietingj

Workflow to extract chunks for a randomer dataset

1

Hi Marcus, We have finally managed to get a dataset that has good coverage of randomers with and without 8-oxoG at the center surrounded by 4 random bases on either...

moa4020

Unknown error in resquiggle command

2

Hi, I am using this command to resquiggle my RNA data: remora dataset prepare pod5_dir file.bam --output-path mod_chunks --refine-kmer-level-table 5mer_levels_v1.txt --refine-rough-rescale --motif CG 0 --mod-base m 5mC --reverse-signal --overwrite But,...

CarolinaA09