Convert RNA STARsolo output to AnnData format


Thank you for creating this community for Galaxy questions. I have been designing a workflow for single-cell RNA-seq analysis. I am using the RNA STARsolo tool to carry out demultiplexing and quantification. It gives me output in tsv (Barcodes and genes) and mtx (counts) format. I referred to this tutorial for converting different scRNA-seq data formats - Hands-on: Converting between common single cell data formats / Single Cell. I went through it and couldn’t find any tool that could convert the tsv and mtx format to AnnData format. I need the AnnData format to run the downstream analysis using ScanPy. I combed through the tools in Galaxy but couldn’t find any tools to do this conversion. Are there any tools that can do this? Thank you!


Hi @Priyanka_Bhandary

Would this tool do what you need? It has a tutorial and extra help down in the Help section on the tool form for more context → Import Anndata and loom from different format