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Hi, I am working with Nanopore direct-RNA sequencing and found your tools really useful. However, while I was trying to use your BamSlam script to generate some summaries and figures for the alignment…
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I have two datasets:
1. SUP-rebasecalled direct RNA with pseudouridine calling, aligned to a reference
2. The same data as above, but now put through reference-anchored inference with remora for p…
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Dear all,
I'm trying to create a h5Seurat object, however, the data that comes out is corrupt.
I updated my datset:
sc
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hello,
Thank you for this package! Is there a way to extract the original cells for both the RNA and ATAC-seq that were used to make the pseudomultiome and map those to the cells for the output mat…
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I really like your preprint and I would love to use it for direct RNA sequencing.
Do you happen to work on adjusting the UNCALLED for direct RNA sequencing? Given that an accurate RNA k-mer model is …
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Dear Greg - thanks for your continued work on this and for this follow up paper with updated pipeline. I'm the lead author of [Hermida et al. Nat Commun 2022](https://www.nature.com/articles/s41467-02…
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We are using the scripts which you published on this paper and repeat the m6A calling using EpiNano, with the datasets published on Nature Communication (2019) including Curlcakes and yeast datasets.
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TTT16 updated
3 months ago
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Running nanopolish eventalign on direct RNA data, basecalled with guppy 3.6.1 with parameters
`--samples --print-read-names --scale-events`
fails with the error
`nanopolish: src/nanopolish_…
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I#m having trouble to understand the naming convention of samples. Some cell lines have missing replicates (e.g. only 1,5,6) and some replicates have only run1 or run2. Would greatly appreciate your h…
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Hello !
I'm performing a multivelo analysis on a complex tissue with more than 10 well-represented cell types. When I perform the analysis on the whole sample, it work just fine.
However, I'm mainly…