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-
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
-
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...
-
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...
-
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 ...
-
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...
-
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...
-
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...