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Tomcxf / FASTdRNA

FASTdRNA is a workflow for analysis of ONT direct RNA seq dataset
MIT License
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Questions about using FASTdRNA #9

Open ldyang14 opened 4 months ago

ldyang14 commented 4 months ago

Hi,

FASTdRNA is an easy-to-use workflow for processing direct RNA sequencing data. It makes the processing flow simple and lets the analyzing steps be done consistently, saving users a huge amount of time and energy. Thank you for this great work first.

But I had some problems using it. Could you help me out with these issues? Thanks in advance. I've listed them below:

  1. Most modules can be executed successfully under one sample but fail for multiple samples. I think the expand function should be used carefully.
  2. The software nanocompore does not seem to be in the environment.yaml.
  3. dRNAmodif_1.py, line 23: Is that a typo? I think file.slow5.idx should be replaced with file.blow5.idx.
  4. dRNAmodif_2.py: failed to execute the rule follow.
  5. dRNAtail.py: The result polyA_results.tsv is empty. I think nanopolish index should be done first for estimating polyA tail lengths.
Tomcxf commented 4 months ago

Thanks for your using our software and valuable suggestions! A1: I am not clear that "fail for multiple samples". For dRNAmain and dRNAtail, each sample should run individually. dRNAmodif and dRNAas need one more samples. I don't know where is your error happened. A2: nanocompore didn't include in yml. Sorry for that, I have updated installation in guidance in here A3: It might make your confused since I use file.slow5.idx as output. It's a tiny skill when using snakemake. In f5c index, {example}.fastq is input file and in fact file.blow5 is the output we assign the software. The output file.slow5.idx is automatically generated by f5c. Actaully the following rule needs file.slow5.idx, so I put it in rule 'index' to make sure this rule can run well :) A4: rule follow actually is running a py. so you can just modification.py ./modification/sampcomp/ referencefile Sometimes it might run into some error when snakemake run python script. I will check later :) A5: nanopolish index has automatically run before run this rule (if you follow main -> poly) you can see that from the output when running. dRNAtail.py is slow due to the software. When you saw the result is empty, please wait for at least 30 min If you have any more questions. please tell me. Hope can help you!!