I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?

Question

[Spring]

"I tried running cell ranger to align the fastq files for SRR9681140 (scRNA-seq, paired, NextSeq 500), but encountered an error message saying 'An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input.' Later, I found out that the SRR9681140 data might not be prepared with the 10x genomics protocol, but rather with a different protocol. I thought that all fastq files could be aligned with cell ranger, but it seems that's not the case. Could the reason for this error be related to the different protocol used for the data preparation?"

If that's the case and I can't use cell ranger, do I need to go through a series of steps like HISAT2, FeatureCounts, and so on to perform alignment?

(Since I'm still a beginner, I appreciate your patience and understanding.)

Answer 1

[ATpoint]

CellRanger is specific for 10x Chromium. I did not check the details of this single-cell platform so I recommend to see what papers that used this platform used for preprocessing.

[fracarb8]

For the paper, they used the indrop pipeline (https://github.com/indrops/indrops), and you should have a look at it, and try to run with the same settings (e.g. Mouse: GRCm38.85)

[Spring]

Thank you very much!

[Spring]

Thank you so much! If the 10x Chromium protocol is not used, should the processing be done with HISAT2, FeatureCounts, and so on?