-
### Description of feature
Use references from CTAT.
Allows to shorten reference building time and maybe call a few more fusions with STAR-fusion as it is optimised for this
-
I downloaded the CTAT-mutations package from https://anaconda.org/bioconda/ctat-mutations in a new environment. I downloaded this github package and tried running the "ctat-mutation-lib-integration.py…
-
When passing the `--rightfq` and `--leftfq` args, the `$ensure_full_path method` is only effectively called on the first file in the list of fastq files (`ensure_full_path` doesn't support lists of fi…
-
Hi,
I'm trying to run CTAT pipeline to annotate my variants, with singularity but I'm having this problem:
```
Missing path to CTAT_GENOME_LIB in $CTAT_GENOME_LIB
```
but I actually have the li…
-
Hi,
I am building a custom genome library for GENCODE ver 36. However, I encountered a problem that indicates there's no "gencode.v36.annotation.gtf.revised.custom.gtf".
I used the latest docker…
-
Hi, we are trying to use your pipeline and encountered a problem while trying to download GRCh38_v27_CTAT_lib_Feb092018.plug-n-play.tar.gz from broad. This file is no longer available (they provide on…
-
Hello,
I've been having multiple issues in Step 3 of the installation process (Execute the mutation lib integration utility). I have directly installed ctat-mutations and all the libraries and depe…
-
Hi,
I'm running ctat-genome-lib-builder with a specific Gencode release using the following paremeters:
```
/software/ctat-genome-lib-builder/prep_genome_lib.pl \
--genome_fa /star_fusion/…
-
I ran into an issue that seemed to be browser dependent but was easily fixed. Basically, I had the wrong path to an HTML file in my training json so the flask serer couldn't find it. When running unde…
-
Hi,
First of all, thank you for this wonderful tool.
I used CTAT_Mutations v3.2.0 in Conda environment and I am wondering why 'subprocess.CalledProcessError' is happening.
the command line is:
…