How to modify the raw fastq file from MARS-seq as in the 10x scRNA-seq format ?

[Chris-lang478]

Hi. In your publication :"Analysis of Alzheimer’s disease scRNA-seq data. The MARS-seq scRNA-seq raw data were download from GSE9896971. The raw fastq file were modified using custom scripts to embed the cell barcode and UMI in the same read, as in the 10x scRNA-seq format. " What's the custom scripts?My raw data is from STRT-seq, barcode is in read1 and UMI is in read2, do them need to be modified to the 10x scRNA-seq format?

[jphe]

Yes， scTE use the bam file generated by CellRanger or STARsolo. In brief, you only need to make your fastq file can be run by those two tools is OK.

The most easiest way is to transfer your fastq file to 10x like format in read1.

[Chris-lang478]

Thanks!