antgomo
antgomo
I am also interested in this approach. I have paired-end bulk-RNAseq with UMIs in order to avoid duplicates. I have three fastq's per sample : 1 UMI, 2 and 3...
Ok, thanks Eduardo Yes I will try imputation. Many Thanks! Toni
Thanks Eduardo, I'll check it hence i will use "classical". Another question is if SUPPA can deal with different numbers in comparison, I mean instead 50 vs 50, 50 vs...
I tried in classical after checking for headers and columns python3.7 ~/soft/SUPPA-2.3/suppa.py diffSplice --method classical --input ensembl_hg19.isoforms.ioi --psi A/A_splicing_matrix.psi B/B_splicing_matrix.psi --tpm A/A_TPM.tpm B/B.tpm --lower-bound 0.05 -gc -c -o DS_SLE_CTRL -nan...
Ok, yes very strange it's not related with python version I guess, could you confirm that point? I am subsetting the data to 20 vs 20 and checking if its...
Sorry again for the continous messages, well i subset the data to 6 vs & and I ran empirical and classical in empirical, everything went right python3.7 ~/soft/SUPPA-2.3/suppa.py diffSplice --method...
Ok, thanks Lars!
> Hi Brian, > > In general, I would argue that one should be cautious with removing PCR duplicates in RNA-seq data (unless you are dealing with reads with UMI...