Hi all,
after I got a dataset analyzed with this archaic ;-) NFCORE-atacseq ( https://nf-co.re/atacseq/2.1.2 ) , I've been asked to look for differences according to the sex of individuals using diffbind ( https://bioconductor.org/packages/release/bioc/html/DiffBind.html ) and I must say, I've no idea of what I'm doing.
So, I've got this samplesheet containing the sample names (Tissue+sex) , the path to the bams and the peaks, I'm not really sure about those "Tissue Condition QC Factor Replicate".
I use the R script below to run diffbind inherited from a colleague who left the lab. Everytime I try to run it, the process is killed even with the following slurm directives:
#SBATCH --job-name=diffbind
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=50G
so my questions are:
1) Is there anything I should change to get the diffbind by sex ?
2) how can I avoid this dba.count error ? I got the same error with bParallel=TRUE
Thanks
