Delaney Sullivan
Delaney Sullivan
You might be able to get it to work — I can compile htslib just fine but I think I needed to use the right C compiler or build in...
That was a mistake, it’s now a lower case v
Hello! I just looked at the dataset -- for some reason, there seems to be strand-bias [causing mapping rate < 30%] under the default 10x settings (forward-stranded) so set --strand=unstranded....
@mortunco I just released a new version of kb-python (version 0.28.1) -- it should cause less UMI differences between the standard index and the nac index. Previously, if there was...
You need to put more fields into the GTF. Take a look at an example for another gene and use that as a template for making your custom GTF entry.
See the end of this manual here (requires pip installing kb_python version 0.28.2): https://www.biorxiv.org/content/biorxiv/early/2024/01/23/2023.11.21.568164/DC1/embed/media-1.pdf Currently migrating this manual to a website, but yeah, kallisto is a great tool for split-seq:...
See https://github.com/pachterlab/kallisto/blob/master/INSTALL.md (You need to have a build directory)
@af8 ``` git clone https://github.com/pachterlab/kallisto cd kallisto mkdir build cd build cmake .. -DENABLE_AVX2=OFF -DCOMPILATION_ARCH=OFF make make install ```
Yes, I agree and I'm working on it. :) We'll need to also reorganize all documentation -- there are around 4 different official documentation pages for kallisto and bustools; we...
I'll at least update the CLI page today though.