Jiang Hao

cpu basecaller --modified-bases m6A

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# Issue Report [error] Too few arguments ## Please describe the issue: [2024-08-05 21:02:10.576] [info] Running: "basecaller" "-x" "cpu" "--modified-bases" "m6A" "--mm2-preset" "splice" "-k14" "--no-trim" "/lustre/home/jianghao/workspace/01.RNA-seq/DM_bulk_ONT/output/dorado/[email protected]/" "/lustre/home/jianghao/database/05_RNA/01_DM_ONT/pod5/LDL-1/pod5_pass_1/" I really can't...

issuesTraceback (most recent call last): File "/lustre/home/jianghao/mambaforge/envs/isoquant/bin/isoquant.py", line 808, in <module> main(sys.argv[1:])

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i check all of requirements.txt, so what's wrong? isoquant.py --test commond line: ~/mambaforge/envs/isoquant/bin/isoquant.py --test === Running in test mode === Any other option is ignored 2024-08-02 21:01:57,137 - INFO -...

Enrichment analysis of non-model plants

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**Is your feature request related to a problem? Please describe.** I want to use omicverse to do Different Expression Analysis, but the species I studied is potato, in R language...

`[ data format: "fastq", { name: "Experiment1", long read files: [ "/PATH/TO/FILE1.fastq", "/PATH/TO/FILE2.fastq" ], labels: [ "Sample1", "Sample2" ], illumina bam: ["PATH/TO/ILLUMINA1.bam"] }, { name: "Experiment2", long read files: [...

m6A methylation analysis and explanation of output files

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## methylation distribution on read I want to analyze the RNA m6A modification. I selected m6A_DRACH model when dorado basecaller. Then I use modkit for downstream analysis. `modkit pileup $bam...

## Can I use custom genome file and gtf file? I want to find fusion transcripts in potato ONT direct RNA sequencing data.

Can't find v0.2.7 on docker hub

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I can't find v0.2.7 on docker hub. Newest version is v0.2.6. 

Transcription factor regulatory network analysis for other species

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# **What files should be input for Transcription factor regulatory network analysis** I want to utilize hdWGCNA to study Transcription factor regulatory network in plants. I have prepared the motif...

Whether the spatial coordinates of integrated SRT data from multiple samples influence downstream analyses?

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I have 9 samples, with three stages and three replicates at each stage. And I use `merge()` function from seurat to merge 9 SRT data. I have completed the basic...