Vicente Yepez
Vicente Yepez
Hi, the external counts (containing the matrices needed for both expression and splicing) can be created using DROP with the rule: `snakemake exportCounts` Furthermore, you have to fill a couple...
1. Raw counts. If you exported the counts using the same gtf file as you are using with the local samples, should work. DROP checks that the number and names...
Hi, we're working on this. We'll let you know once it's done.
We've never seen that error before. Two things that come to my mind: - be sure you have `filter: true` in the `aberrantSplicing` dictionary in the config file - be...
Also have a look at the Counting summary html (`Output/html/Scripts_AberrantSplicing_pipeline_Counting_DatasetsF.html`). How many junctions do you originally count? How many are there after the filtering? It should look similar to this:...
Hi Jeffrey, To check your resources, can you please run the following in the terminal: ``` free -m -h # look at the Mem row lscpu # look at the...
It seems all your junctions were filtered out. Can you run: ``` library(FRASER) fds
Can you please run the following: ``` library(FRASER) fds
can you replace the second line in the code I sent you with: ``` dataset
Hi, I see 2 potential problems: 1. Due to the small sample size, there might not be any significant results with the default cut-offs. Which deltaPsi and padj cutoff values...