search

thelingxichen / scSVAS

scSVAS (scDNA-Seq Somatic Variant Analysis Suite)
https://sc.deepomics.org/
4 stars 0 forks source link

Using scSVAS with Cell Ranger Output #4

Open Romeo1-1 opened 2 years ago

Romeo1-1 commented 2 years ago

Hello,

Thank you for this package/website. I tried running a few analysis on my scDNA samples with SCYN and i had no issue.

I'm currently trying to run analysis but directly with the outputs of Cell Ranger (meaning h5, bed files & loupe output).

1) What scripts should i use in your script to get "the maximum number of analyses possible" ? I tried using bed2matrix.py ; get_group_from_dloupe.py & process_10x_h5.py, but would using other scripts allow me to use more functions ?

1bis) I've encountered the same issue as @Suzuk1 a few months earlier. When i run process_10x_h5.py, i receive the error ImportError: cannot import name 'genome' from 'biotool' (unknown location). I tried searching on the internet but i couldn't find any help on biotool & genome. I also have the same problem with from utils import phylogenetic as phylo, i receive the same kind of error.

1ter) I also tried running scVAR.py (as i understand it's like a light offline version of scSVAS) but i receive the same errors as running process_10x_h5.py.

2) I tried using the output of bed2matrix.py on my node_cnv_calls.bed file on the website, but i receive an error saying i'm not processing a valid file. Am i using the good Python function ?

Thank you a lot again for your package/website,

PS : I'm running Linux Ubuntu on WSL2. And i had no issue with get_group_from_dloupe.py

Romeo1-1 commented 2 years ago

After some more research, i think it's because the utils & the biotool i installed via pip don't contain "genome" and "phylogenetic" submodule. On the other hand, i couldn't find any way to "circumvent" this problem. Do you have any idea ?

Thank you in advance,