yeroslaviz

up-to-date with GATK 4

How are the gene scores calculated?

20

In the new version you calculate the cell sets over gene scores. How are these scores being calculated?

Hi, in notebook 1 you offer the possibility to calculate gene scores, as well as to work with the pre-defined cell-sets. What if I have different gene-sets, i have calculated...

trajectory plots unidentifiable.

2

Hallo again. I'm honestly impressed by the modifications and fixes you're doing to the program. Thanks a lot for that. I would like to better understand the trajectory and trajectory_trends...

import error "from scipy.sparse.sputils import IndexMixin"

1

After installing version 1.0.2 and running the command ``` wot optimal_transport --matrix data/ExprMatrix.h5ad --cell_days data/cell_days.txt --out tmaps1.0.2/tmaps1.0.2 ``` I get the following error ``` Traceback (most recent call last): File...

small corrections in command line examples

3

in calculating the [Trajectories](https://broadinstitute.github.io/wot/cli_documentation/#trajectories): - The command option `--out` should be modified to be the output file prefix. If I uses this `--out traj.txt`, it creates a file with the...

Is it possible to add the option to run an enrichment analysis directly on Ensembl IDs. For now, each time I need to convert my mouse Ensembl IDs to Entrez...

Hi, I was wondering, if it is possible to use SPAdes to identify possible transgenic sequence within a genomic genome. We have done a WGS on transgenic animal, which was...

error with bambu for a big file

3

My bam file was mapped with `minimap2` using the `-ax splice` option against the reference genome of C. elegans. When trying to quantify the data I get the following error:...

When running talon with my three samples i get the following error: ``` $ talon --f Analysis/talon/FAT11673.config --db Analysis/talon/WBcel235_gtf_talon.db --build Cel.WBcel235 --threads 12 --o FAT11673 [ 2022-08-19 11:15:36 ] Started...