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vertesy / pseudoBulk

Cluster-specific pseudo-bulk analysis of 10X single-cell RNA-seq data by connecting Seurat to the VBC RNA-seq pipeline.

https://vertesy.github.io/pseudoBulk

MIT License

9 stars 2 forks source link

To Do #1

Open vertesy opened 4 years ago

vertesy commented 4 years ago

Milestones to finalize the pipeline

[x] Barcode export from Seurat
[ ] Barcode de-duplications
[ ] Find the cause of repeated qNames in the 10X aligned bam file

Barcode de-duplications

[ ] Explore: is it done by 10x ??
[ ] Find solution via 10X or alternatively via a python script

Possible future improvements

[ ] Use the exact same index & reference to what 10X cell ranger uses.
[ ] Make it directly executable directly on a 10X output folder (using the clustering that 10X does).

Using the exact same index & reference

→ This is actually needed if you want to analyze 10X runs that have been mapped to the pre-mRNA reference

When you run the VBC RNAseq pipeline, provide the gene model (GTF) and the exact same human genome the use (you have to directly link both).

--gtf to use exactly the same names
- if you provide both --gtf and --fasta it recreates the reference, see:
- both --gtf and --fasta and--saveReference but not --genome to save the custom reference
- Pass on to Maria → add it to the cextflow config