Eric Johnson

Attempting to load EMBEDR after a clean install in the main directory of this repo: `from EMBEDR import EMBEDR` causes the following error: ``` Traceback (most recent call last): File...

n_jobs is only being applied to the Affinity matrix calculation.

Question about read aggregation by barcode

3

Hi! I am attempting to run TRUST4 on a single-cell V(D)J data set and it is running rather slowly, so I was peeking under the hood to see if there...

Unrecognized option '--UMI--barcode': annotatorArgs improperly concatenated

1

Hi! I discovered a wonderful bug. If you make a TRUST4 call with the `--UMI` specified before the `--barcode` as in the example below, the `annotatorArgs` in `run-trust4` becomes `--UMI--barcode`...

How is `cid_full_length` assigned?

3

So I've been trying to understand how the `_report.tsv` is generated from the `_barcode_report.tsv` and the `_cdr3.out` files in the `trust-simplerep.pl` script and I believe that I have correctly determined...

Pandas error after correcting UMIs

1

Everything looked to be running fine: ``` !CITE-seq-Count \ -R1 $Hash_R1 \ -R2 $Hash_R2 \ -t feature_barcode_onlist.csv \ -cbf 1 -cbl 16 \ -umif 17 -umil 28 \ -wl 737K-august-2016.txt...