Anna-Leigh Brown

Extra tags + HISAT3 +

6

Hola - So what I want to do is reproduce GRAND-slam's method for calculating NTR without having to use GRAND-slam. I think the tags generated by NGM would easily give...

homebrew/science is been deprecated - manual on Seqan website still advises install with brew install homebrew/science/seqan

4

Is it possible still to install seqan with homebrew? @rrahn It seems that homebrew/science is been deprecated, and that seqan (the library) migrated to homebrew core and that seqan-apps disappeared....

Merging bams for including novel splice sites makes a really big bam :(

11

Hi, I have about 30 samples which I want to do a differential splicing analysis on. The instructions for including unannotated splice sites suggests that I first merge all my...

Tutorials are quite outdated

1

The notebooks as they stand are from Julia 0.5

Hello, While running I occasionally get warning messages on some of my samples "mafR not sufficiently small" "mafR

imputing across conditions vs within conditions

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Thank you so much for your creation of this wonderful tool. I am brand new to analyzing mass-spec data, and have trying to get my head around how to best...

'main' panicked at 'index out of bounds: the len is 1 but the index is 1'

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Built the index first using gencode v40 ``` mudskipper index --gtf /SAN/vyplab/vyplab_reference_genomes/annotation/human/GRCh38/gencode.v40.annotation.gtf --dir-index /SAN/vyplab/vyplab_reference_genomes/mudskipper_indices/human.gencode.v40 ``` And then tried to convert with ``` mudskipper bulk --index /SAN/vyplab/vyplab_reference_genomes/mudskipper_indices/human.gencode.v40/ --alignment my.sorted.bam --out my.mud.bam...

What does it say about our data that the m6a RNA modification rates seem somewhat low?

4

Just a question about motif searching and data quality. Our data is called using dorodo and we called the bedmethyls with modkit pileup We tried using the defaults but consistently...