Kennedi Todd

icon company TGen icon location Phoenix icon location Bioinformatician in the Fryer Lab at TGen in Phoenix, AZ

Results 12 comments of Kennedi Todd

install seuratWrappers failed

I had the same problem

tombo text_output browser_files outputs succinct error

@adalisan did you find an answer for this?

tombo text_output browser_files outputs succinct error

@adalisan ah thanks! a container is exactly what I have been looking for

coloring individual nodes

@SchmidtPaul Thank's for this code! It worked perfectly. I needed to specify the package (sankeyD3::sankeyNetwork) since I had networkD3 loaded too. Excited to see the improvements you will make with...

lima ERROR: [pbcopper] alarm ERROR: cannot write to empty alarm filename

> Someone needs to upload a file to reproduce. https://github.com/PacificBiosciences/pbbioconda?tab=readme-ov-file#file-sharing Checking to see if I'm allowed to share the file security wise. I learned that demultiplexing was already done on...

lima ERROR: [pbcopper] alarm ERROR: cannot write to empty alarm filename

I have permission to share my BAM file now. However, the file drop off link on the README appears to be down.

Trouble with Tombo pipeline for RNA-Direct Sequencing

@Lucas-Servi Did you ever get this working? This is what I have done so far. I don't think you are converting fast5 files correctly. Tombo requires single-fast5 files (one read...

ERROR: 'utf-8' codec can't decode byte 0x8b

@sagnikbanerjee15 I have the same issue. Did you ever find a solution?

ERROR: 'utf-8' codec can't decode byte 0x8b

> No sorry, I had to give up. @sagnikbanerjee15 I had this error with a gzipped file and fixed it with gunzip. Are you sure your file is named correctly...

tombo installing error by pip

@gaoxiangcao I am working on modification calling and got up to preprocess to work. I'm currently resquiggling but it's taking a while to run. Here are the steps I have...