Missing LinearCount and CircSkipJunctions files
mumichae opened this issue · comments
Describe the bug
More a question than a bug.
When I specify -D
and -G
, I don't get LinearCount
or CircSkipJunctions
, even though all necessary files were provided. Is this a bug or am I missing something?
To Reproduce
$OUT_DIR=output
DCC Chimeric.out.junction \
--mate1 mate1_Chimeric.out.junction --mate2 mate2_Chimeric.out.junction \
--annotation gencode.v38.annotation.gtf \
--bam Aligned.sortedByCoord.out.bam \
--refseq hg38.fa
--D -G --chrM --rep_file repeats_hg38.gtf.gz \
--output $OUT_DIR --temp $OUT_DIR/tmp --threads 5
Conda environment YAML
name: DCC
channels:
- conda-forge
- bioconda
dependencies:
- python=3.8
- pip
- HTSeq
- pysam
- numpy
- pandas
- pip:
- https://github.com/dieterich-lab/DCC/archive/refs/tags/v0.5.0.tar.gz
Desktop:
- OS: CentOS
- Python version 3.8.12
- Version 0.5.0
Hi @mumichae,
Your command line seems good, but given that you provide mate1+2, you should specify -Pi
. There might be an issue checking the flags accordingly.
Let me know is that helps.
Cheers,
Tobias
Hi Tobias,
Thanks a lot! I must have missed that one, now it works!
Best,
Michaela