Ruiqi-CUB

Trimming customed adaptor sequences

1

Hello! Is it possible to trim the customed adaptors using trimmomatic for exon capture sequencing? If so, how can I create the adaptor fasta file (sequence header etc.)? The adapters...

How to get the node number

1

Hi Dr. Yu, I am trying to annotate my tree in ggtree. Do you happen to know How I can get the node number? Is there a way to plot...

ko2name function doesn't work on some pathway numbers

2

Hi Dr. Yu! I was trying to use `ko2name` fuction to get the name of pathways with pathway numbers. I found a lot of pathway numbers don't work with `ko2name`...

Hi David! I am using OrthoFinder output for CAFE and I would like to know the functions of the orthogroups that are expanded or extracted. I annotated each genomes used...

Hi David! Thanks for developing this awesome tool! I would like to use the OrthoFinder to just build the gene tree and species tree. Would it be possible? I have...

gffread -w works but not -x and -y

2

Hi there, thanks for developing this very useful tool! I tried to use it to extract CDS and protein from a genome and corresponding gff file. It works with `-w`...

Adding contents related to personal/lab server

1

Plenty of labs are still using personal/lab/departmental servers as their primary computing resources. It would be helpful to add the option here and to compare it with cloud computing.

WGCNA choosing softpower

1

Hi there! Thanks for the tutorial! I got the following figure following WGCNA tutorial: Which softpower should I choose? 5? Thanks a lot!

Hi Marcela, I am trying to pull the mitochondria genome from the PacBio raw reads using MitoHiFi. I did not find any mito genome from closely related species, but I...

No output after successfully running the pipeline

1

Hi Marcela! I am trying to run MitHiFi with the testing data, the log file shows the pipeline is done, but no files were written to my working directory except...