m6anet

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Modification of n_read_per_site

3

Hi. I currently run m6Anet with pre-trained model (Hct116_RNA002). I wonder if there is any way that I can change the n_read_per_site from 20 to 10. I changed n_read_per_site in...

DayeaPark

Hi, I'd like to run a benchmark of the available m6anet model weights. Can I get a list of test set genes (ensembl id) for the benchmark? Thanks.

vadanamu

transcript_position column header from data.site_proba.csv output file

1

Hi team, I would like to have clarity on the column header _transcript_position_ in the output file of _data.site_proba.csv__ generated after the command _m6anet inference_. Does it indicate the position...

gsukrit

DRACH sites at the beginning or end of sequences

1

Hello, In my data, I have two DRACH sites that are at the start and end of an RNA sequence (i.e., two bases from the start of the sequence and...

tjprins

Reproducing Fig 2d,e; request for transcriptome2genome.py for dummies

2

Hi @chrishendra93, I'm trying to reproduce part of Fig. 2d and 2e using the HCT116 and VIRC models provided in Git to verify that my installation of m6anet is intact...

hengjwj

m6anet dataprep error

3

Dear developers, I've already successfully run the full m6anet pipeline (version 2.0.1) on a given dRNA-Seq dataset, but now am experiencing the following error during the dataprep step on a...

eltonjrv

Disconnect between site and individual read mod probability RNA004

1

Hello, Thank you for creating this easy to use tool! I've used it in the past for my RNA002 data, and it has worked very well. I just generated some...

esh97

f5c or nanopolish

3

Should we use f5c or nanopolish for indexing and eventalign, if our reads are RNA002?

JSluo888

probability_modified and mod_ratio are 0

2

Dear Developer I was recently trying to analyze one of the HEK293T datasets using m6anet and I have some questions about the results. Some of the sites in the results...

lbwfff

Arabidopsis VIRC instead of col0 (wild type)

3

I am wondering if there is any reason that you trained and compared the model using the virC dataset (rescued) instead of col0 (wildtype) dataset for Arabidopsis?

haotianteng