10xgenomics / enclone Goto Github PK

Dear developers,

I wanted to use your tool enclone on 2 bcr files from 1 donor, before and after treatment.
However, I get following message:

Significant barcode reuse detected.  If at least 25% of the barcodes in one dataset
are present in another dataset, is is likely that two datasets arising from the
same library were included as input to enclone.  Since this would normally occur
only by accident, enclone exits.  If you wish to override this behavior,
please rerun with the argument ACCEPT_REUSE.

Here are the instances of reuse that were observed:

bcrPBMC_JUQ064_hg19, bcrPBMC_JUQ065_hg19 ==> 245 of 972, 829 barcodes (29.6%)

The barcodes don't have a prefix or suffix, so it's only normal that some are present in both.
Is there an argument I can set that adds a string to the barcode using the META csv file?

Thanks in advance,
Aurelie

I'm doing some testing with enclone for generating honey plots and it works nicely. I'd like to add a custom variable (eg, annotated cells for each barcode) and color according it. Is there any way to do it, please?

Also, does enclone generate any kind of file, table or whatever for importing it to R and graph the honey plots more aesthetically?

Thanks in advance.

GIF above for demonstration of bug. enclone runs without issue in OS X Terminal (zsh shell), but won't display properly when Terminal is in full-screen. Issue is replicable using the bash and csh shells.

Possible confounder: this is on a machine running OS X Catalina. Needs to be tested on somebody else's Mac at a minimum, unsure if this will happen on Windows.

I compiled enclone using rustc 1.40.0 (73528e339 2019-12-16).

Hi! I am trying to run the scoper code used in the enclone paper, with a new version of the immcantation container, that fixes the parallelization issue you refer to in enclone/enclone_paper/src/scoper/autopilot.R.

Should build_immcantation_inputs in enclone/enclone_paper/src/scoper/autopilot_master.sh be build_clonotyping_inputs?

I am new to rust and I am figuring things out. It would be helpful if you could provide a little more detail on how to reproduce the analysis, in particular adding instructions on paths from where to run things, and when/how to use cargo, rustc...