Hello,
I am having **difficulties aligning** fastq files from sample **AD9** (**syn12514624**)
For each cellranger count chemistry option the whitelist of barcodes does not match those in the AD9 fastq files and therefore alignment is unsuccessful.
All other samples have been processed correctly.
Has anyone else using syn12514624 single-cell RNAseq data stumbled into this problem?
Created by Michael Vermeulen michael.vermeulen Interesting! Thank you for sharing what you found. thank you. I have confirmed that the paper you have linked is the paper using the available ROSMAP microglia single cell data .
I was confused that sample numbers and disease states did not match up, however not all of the samples used in the linked study are ROSMAP participants.
For future reference to others using the data, AD9 FASTQs do not align using CellRanger v3, however they do successfully align using the recently released CellRanger v4 (and CellRanger v2).
I have found a bioRxiv paper referring to this dataset [here](https://www.biorxiv.org/node/104512.abstract). If this is unable to answer your question, Vilas Menon, an author, should be able to help. Please let me know if I need to reach out to him for assistance. Thank you!
I am unable to answer your initial question, but am asking around to see if I can find someone who can help.
As for whether there is a paper associated with that data, I would have to look into that and get back to you. Does anyone know of the paper associated with syn12514624?
The protocol is provided above the fastq files, its unclear to me if there's a publication.
If anyone could provide this publication info or the authors who produced the data that would be great.