KunFang

Hi, Thanks for providing this awsome command line tool. I was wondering if it is possible to add -p paramemter for mkdir (no error if the folder exist) and -r...

Too many DEGs?

1

Hi, I am a fresh user of glmGamPoi and thanks for providing this awesome tool! I tried to identify DEGs in scRNA and successfully run the following code: ``` load('/Volumes/kfsd/GSE200903_new_combined_cluster_FibroSamples_2022-01-14.RData')...

ImportError: cannot import name typeDict

4

Hi, Thanks for providing this useful tool! I tried to run tutorial but with the following error ``` MAESTRO scrna-init --platform 10x-genomics --species GRCh38 --cores 8 --rseqc --directory pbmc_1k_v3_fastqs --count-cutoff...

Failed to get modification model

1

Hi, I met a error when run dorado basecaller hac,5mCG_5hmCG,6mA output_01.pod5 > test2.bam ``` (base) kfang@icrc4lcga001:~/data/kfang/NucPatternOri/ONTdata$ dorado basecaller hac,5mCG_5hmCG,6mA output_01.pod5 > test2.bam [2024-09-27 21:23:11.650] [info] Running: "basecaller" "hac,5mCG_5hmCG,6mA" "output_01.pod5" [2024-09-27...

Dear RERIO team, Thanks for providing this wonderful repository! I am actually not sure if this is the right place to ask but I am very new to Nanopore base...

Hi, I wondered if there is a way to keep multiple mapped reads. Thanks in advance! Best, Kun

Chunk process for summary and sample-prob

3

Hi @ArtRand, I was wondering if it might be possible to add chunk-based processing (similar to the pileup method) for the –no-sampling option in summary and sample-prob in the future....

How to calculate filter thresholds from probabilities.tsv

6

Hi @ArtRand , Thanks for your continuous help! I have a naive question about how to calculate filter threshold from probabilities.tsv (generated from sample-probs). In documents, it says ``` Filtering...

How to finetune [email protected]_6mA@v1

1

Hi @marcus1487 , Thanks so much for your support! I would like to explore fine-tuning the latest 6mA model by incorporating a custom control dataset. I reviewed issue #171 regarding...