micmin3 / hpv_opscc_analysis Goto Github PK

Hi there,
I am currently working with GSE182227 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182227), produced from your nature paper in head and neck cancer (PMID: 37012457). I am new to bioinformatics.

I just wanted to confirm if there's a mixture of single cell chemistry used in GSE182227? The paper stated that V2 chemistry was used: "Samples were processed using the Chromium Single Cell 3’ (v2 Chemistry), and in two cases 5’, platform with the target of ∼10,000 cells (10x Genomics)"

However, when I am running STARsolo alignment using v2 chemistry, I do get errors in only some SRR files "EXITING because of FATAL ERROR in input read file: the total length of barcode sequence is 28 not equal to expected 26" -suggesting that it may be V3 chemistry. Whereas, when I used a V3 whitelist, it seems to solve the error.

Hope you can help!

Thanks
Kenny