Missing LinearCount and CircSkipJunctions files

mumichae commented 2 years ago

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

tjakobi commented 2 years ago

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

mumichae commented 2 years ago

Hi Tobias,

Thanks a lot! I must have missed that one, now it works!

Best, Michaela

dieterich-lab / DCC

Missing LinearCount and CircSkipJunctions files #98