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2.3 years ago by
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Recent Replies
Answer: Which aligner is more suitable for ONT R10.4.1 Dorado-corrected reads: minimap2
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Just a very brief summary of the results using the latest versions of minimap2 and winnowmap (by `samtools stats`).
It seems that winnowma…
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great response. thank for mentioning this one. Ill definitely try oarfish. would you recommend running it with the raw sequencing files or…
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Thanks for the comment. I am aware of the workflow. I saw they use StringTie for quantification. I've had good experience with the pseudo-a…
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I needed to be aware of queue channels which you can read about here:
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I am looking back now, and it appears that the files processed after kmer correction (rcorrector) seem to match up, except the first sample…
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People publish predictive papers all the time that have zero experimental support. There are different degrees of "lacking experimental val…
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You should give the reviewer something. An independent way of in silico validation, other supporting analysis. Just "no" might lead to reje…
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I believe ONT recommends Minimap2. This is also the default tools in their EPI2ME workflow.
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In case you were not aware ONT also provides a transcriptome workflow for long reads: https://github.com/epi2me-labs/wf-transcriptomes
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Either do experimental validation, or say that not possible due to lack of collaboration, infrastructure, lab background. If they reject, s…
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As @atpoint suggests, you must align against the transcriptome. Also, the other relevant flags should be set (i.e. `--secondary=no` will di…
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Yes, must strictly be transcriptome. Reference from developer: https://www.biostars.org/p/9556364/
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