Anna Alessandra Monaco, PhD

icon company Max Planck Institute for Molecular Genetics icon location Berlin icon location Computational Biologist with expertise in Molecular Genetics, Evolution, and multi-omics data analysis.

Results 4 issues of Anna Alessandra Monaco, PhD

Applying Salmon Alevin to other single-cell modalities

7 comment

Hello! This might be an unusual request, but I have been attempting to use Salmon Alevin for mapping of **scATAC-seq data** (10X Genomics platform) and have a few questions on...

alevin

Question: how to improve cell barcode correction?

2 comment

Hi, I have been having issues recovering the same amount of cell barcodes post correction in salmon alevin compared to cell ranger. Maybe alevin-fry can help in this task? **What...

Making blacklist for susScr11 with few input bams

1 comment

Hi, I am woking on a evodevo project and I need to compare mouse and pig ATAC-seq data. For the basic qc of the ATAC I wanted to remove blacklisted...

Issues with loadFry() ('x@assays' is not parallel to 'x')

Dear Devs, I am having some issues loading the output of `alevin-fry` scRNA-seq quantification into R; I have used all the following packages in the past without issue. I get...