Nihir Patel comments

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                                            Nihir Patel

bwameth pipeline skipping all bwameth steps when --fasta, --fasta_index, and --bwa_meth_index are provided.

I created the bismark index and kept the reference file within the folder ( not soft link), then re-ran it using --bismark_index and that seems to solve it for now.

error message "can't set using a multi-index" when running example data

Downgrading pandas to 1.0.0 and matplotlib to 3.1.3 resolved the same error. Hope that helps.

Understand above_error_rate and why it's always False for insertion

Thank you for the detailed explanation. "Could you revise the percentage of each insertion and the quality of those reads?" Do you mean to update the threshold? I do not...

Understand above_error_rate and why it's always False for insertion

Thanks again. I do notice that most of the insertions occur near the beginning and away from the cut sites. How can this be addressed? See example below, I do...

Understand above_error_rate and why it's always False for insertion

Thank you for the quick response! I think using a custom config file should be straightforward. ’ll give that a try and update Also, for my reference sequence, I included...

Understand above_error_rate and why it's always False for insertion

Hello Again, I re-ran the analysis with trimming 5–10 bases, but it didn’t improve the results. Looking further into the data, I noticed a position with both a 1-base G...

Understand above_error_rate and why it's always False for insertion

Here is one more from a completely different experiment. As you can notice rate of insertion is very low, even then NONE of the insertions were identified as "above_error_rate"? Would...

Issue with setting up environment for Fine-tuning on Pre-trained Model for Cell-type Annotation

if it helps, I have scvi: 0.20.3, python 3.10, torch.version: 2.1.2+cu121 and so far, it's been working fine