Chang Kim

Is dims.use actually working in RunHarmony?

7

Hello, I noticed the output RunHarmony (Seurat) has all 50 components from PCA, but I specified only using the top 10. Also when I specifically computed only 10 PCs and...

Pair consensus decoding for sequences with the same UMI

3

Hello, I'll be soon getting data RNA-seq data with UMIs, and I was interested in running pair consensus decoding on the data. I noticed the paper's and bonito's implementation takes...

Hello, I was wondering if I can just sum up the intronic TPM reads and spliced TPM reads for a gene for a bulk RNA-seq sample? This is using the...

batch_var doesn't work with vst.flavor = 'v2'

2

Hello, When I set vst.flavor = 'v2' and batch_var between two different batches I get: `Error in fit$Beta[, "Intercept"] : subscript out of bounds` Thanks, Chang

Error in setDataExpr

2

Hello, When I run setDataExpr I get this WGCNA error: ``` Error in WGCNA::goodGenes(datExpr, ...) : datExpr must contain numeric data. ``` I run NormalizeMetacells and have checked the data...

Racon compatibility?

11

Hello, I was wondering if you planned on implementing racon within the tool? Or maybe an output that racon can take? Thanks, Chang

Models for NovaseqX?

1

Hello, I was wondering if there was a possibility for models on the new NovaseqX platforms? Or is the Novaseq6000 error model good enough? Best, Chang

cannot create std::vector larger than max_size()

7

Hello, I attempted to run clustering of reads on my fasta reads, but it terminates after a few minutes of starting. ```Reading fasta file... Done terminate called after throwing an...

Python bindings?

1

Hey Kristoffer, I was wondering if you were considering making python binding of ultra similar to mappy for minimap2? Thanks, Chang

syncmers?

1

Hi, I was wondering if you considered using syncmers (I believe it's already implemented in minimap2) to map the genes between different species? I believe synmcers are specifically meant for...