Avatar

Valentin

  • Total activity 14
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 4
  • Subscriptions 3

Activity overview

Latest activity by Valentin
  • Avatar

    Valentin commented,

    Thanks for the feedback Genevieve-Brandt-she-her.  Terra requires a google billing account, to be linked to, right? I'm currently on that

  • Avatar

    Valentin commented,

    Hello Gatk-team Genevieve-Brandt-she-her, so I figures the more important questions in this issue are: Does the mitochondrial Pipeline work on merged bams? Is that tested or known? Does it allow o...

  • Avatar

    Valentin created a post,

    MitochondriaPipeline on merged Bams

    Hi everyone,  i'm trying to analyse a single cell ATAC-seq dataset of bams with ~2000 cells/bam files, using the MitochondriaPipeline. While only ~600 cells or bams interest me, i figured it's near...

  • Avatar

    Valentin commented,

    Thanks Beri, indeed the thread solved that problem. What now came to me that the bam file (SRA ID: SRR4420337) i am trying to use has no read groups declared, and no @RG line in it's header.  This ...

  • Avatar

    Valentin commented,

    Hi Beri ,  thanks for the quick help! Now running the pipeline my stderr.background file looks as follows: " INFO: Failed to detect whether we are running on Google Compute Engine.10:21:45.788 INFO...

  • Avatar

    Valentin commented,

    Thanks Beri,  So ALL files in the inputs.json need to be downloaded, that's something i wasn't aware of. However in the various google cloud buckets mentioned in the tutorials I could find the need...

  • Avatar

    Valentin created a post,

    mitochondria_m2_wdl: MitochondriaPipeline Issues

    Hey everyone,  i'm student of the ExBio Lab of TUM & new to using GATK. I'm having issues with running the Mitochondrial Pipeline locally. Versions: Cromwell: cromwell-51.jar GATK: gatk.4.1.8.0 Com...