Vicente Yepez

Hi Chris, so all looks good, the number of junctions, splice sites and reads. It is fine if there are rows with all 0 non-split reads in splice sites, that...

Hi Chris, how did it go with the 10 samples?

Good that at least it worked after setting the q. Can you try to run the demo?

Hi @chrisodhams, do you have any updates on this? I think you were able to successfully run it, or?

Hi, Thanks for using DROP and reporting this. It would be interesting to see the results for all 3 of the junctions involved in the exon skipping event you are...

Hi, hard to say. Can you try loading the FRASER dataset located inside `/gpfs/commons/groups/clinical/pkrithivasan/CBI-342/GEN_n16_GTEx_n50_AS/Output/processed_data/aberrant_splicing/datasets/savedObjects/fraser/` in R and checking its dimension? Another idea would be to try rerunning with `minDeltaPsi: 0`

Hi, it seems the values of the GENE_ANNOTATION column are missing for the external counts. It should be: `gtf108` to match your gtf file. Have a look here: https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html#external-count-examples You...

Hi, the error seems to be in the mergeCounts_R rule. A potential reason is that the gene annotation used to generate the external count matrix is different from your provided...

oh true, that folder will only be populated after you count. Check that all BAM files exist and they have a corresponding index file (.bai). If they all exist, execute...

Hi, sorry, I don't understand whether you have executed the pipeline partially or not. Can you execute: ``` snakemake -n aberrantExpression ```