mpiersonsmela
mpiersonsmela
I had the exact same problem. I will try downloading https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/refseq_r80/mc9nr/gene_based/hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather and see if it works. You really should update the index page, I wasted a lot of time before...
The input command was: naive_new_reg
OK, I'll upload the example data tomorrow. Regarding the filtering, I'm removing all the loci that have zero reads for all samples in a group. This filtering strategy worked OK...
OK, I uploaded the files to your Dropbox link. I wasn't able to figure out how to take a small portion that replicates the results, so I just uploaded the...
Thanks! I'll follow up with you by email about collapsing strands.
Regarding collapsing strands, does this basically mean treating each CpG site as one genomic coordinate? I am not sure this would be appropriate for me, since I expect a substantial...
Agreed. UBB is definitely not a transcription factor.
It's 2023, and I still have the same question.
What I did was added the sequences to the reference genome and then used the --fasta option for input. You can find the sequences here: https://neb-em-seq-sra.s3.amazonaws.com/grch38_core%2Bbs_controls.fa
I am also having this problem, only when running on GPU (CPU works OK). The error trace is: `./run_segmentation.sh 2024-09-30 13:35:19,050 - INFO - ** TORCH MPS version installed and...