Hi Drop Team,

I am trying to run and drop some blood RNAseq data. Since I do not have enough control samples, I am using the UDN strand-specific Baylor external count matrix: https://zenodo.org/records/3963470

I had two questions regarding this:

I am using the exact Gencode version 34 GTF used for the Baylor count matrix (and hg19 FASTA for alignment of my BAMs). The GTF I used was downloaded as follows:
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh37_mapping/gencode.v34lift37.annotation.gtf.gz

In my sample_annotation.tsv, I use 10 local BAMs and add the 125 controls from the external count matrix

Running the snakemake pipeline, I get the following error:
Error in rule AberrantExpression_pipeline_Counting_mergeCounts_R:
Error: The rows (genes) of the count matrices to be merged are not the same.

It was previously pointed out #284 #584 that the external count matrix does not have genes from chrMT, which might be the cause of this error. Would you recommend that I try to edit this count matrix? Or is there a GTF file that works with this external count matrix?

The blood count matrix doesn't have the correct format to run aberrant splicing #439
Is there a way to generate the SPLICE_COUNT_DIR with
k_j_counts.tsv.gz
k_theta_counts.tsv.gz
n_psi3_counts.tsv.gz
n_psi5_counts.tsv.gz
n_theta_counts.tsv.gz

as required by the pipeline, using the current available count matrix?

Thank you for your help!