MjelleLab

Download fasta file

10

Hi, I wonder where I can access the fasta files of the genomes for the RNA-viruses within Serratus.

Only one sample when reading multiple files

1

I have a list of MAFs that I combine using the merge_maf function. However, the individual samples are not separated in the Mac object. The samples where created first by...

Improve methRead input validation

7

I have a `methRead` object that is further merged using `unite`. It consists of 5 samples. When running `clusterSamples`, I get the following error: > clusterSamples(Unite.object, dist="correlation", method="ward.D", plot=TRUE,) Error...

In the paper you say that approximately L-k unique k-mers per each read is a good measure that the taxa is truly present in the dataset. When analyzing my WGS...

Problem with "Unknown option: af_gnomad"

1

I have a problem with VEP it seems. Complaining about Unknown option: af_gnomad perl ~/software/vcf2maf-1.6.21/vcf2maf.pl --ref-fasta /home/local/xxxx/.vep/homo_sapiens/102_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz --input-vcf PANCNGS-006.vcf --output-maf PANCNGS-006.vcf.maf --tumor-id T-PANCNGS-006 --normal-id N-PANCNGS-006 --vep-path /home/local/xxxx/anaconda3/bin STATUS: Running VEP...

Keep cluster IDs when converting using as.cell_data_set

1

Hi, I wonder if it is possible to keep the cluster IDS (monocyte, T-cell etc) when converting from a Seurat object using the as.cell_data_set function?

Invalid h5Seurat file: cannot find attribute 'version'

3

Any ideas what this error means? LoadH5Seurat(file = "all_samples_aggr.h5ad") Validating h5Seurat file Error: Invalid h5Seurat file: cannot find attribute 'version'

t_vaf is not included in my merged mag object, so I wanted to calculate it using the formula below. However, the column that is being created is not recognised by...

Is it possible to add a colour to scale_alpha_continuous so that it is the same as the colour of my fills. I have two rings in the tree with colour...

I would like to add a geom_hilight for each phyla from the tip all the way to the root of each phylum. Here is my script and the table below...