Doesn't Work!

[taeyon998]

I tried running your example line (below), but it doesn't work. I tried the other BAM files as well, but they all threw the same error:
Error in if (ARGS$mapping-quality < 0) stop("Mapping quality threshold must be non-negative") : argument is of length zero

I followed the installation procedure given in the manual here: https://cibiv.github.io/trumicount/manual.pdf
I even tried it on different linux servers, all to no avail.

Below are all the steps that I took:

[fgp]

I'll look into it. Which version of R did conda install?

[taeyon998]

I'll look into it. Which version of R did conda install?

R version 4.0.5

[rouzki]

Hi everyone,
Is there any work around this? getting the same error!

[fgp]

I looked into this. The problem is caused by the "docopt" library which TRUmiCount uses to parse command line arguments, which silently changed how it handles arguments containing a dash ("-"). I'll fix the issue as soon as possible!

[fgp]

I have pushed version 0.9.14 to github which should fix this issue.

While testing, I also noticed that our modified version of umi-tools no longer works when freshly installed via conda due to a dependency conflict. I'll look into this issue, and update the conda package ASAP.

[taeyon998]

It seems the modified umi-tools doesn't work yet. This leaves us with only the choice of using a tab-separated file as input.

Could you help us share an example of the tsv input file? It says

The table must be tab-separated with one row per UMI and contain at least the columns “sample”, “gene”, “reads”

A screenshot of such tsv file would be great, so that we can refer to it. Thanks!