Question about paired-end 10x genomics data

[Yunuuuu]

I have 10x 3' sequencing paired-end fastq files, both read files have 150bp (Just like this https://www.biostars.org/p/9529864/), the first read file contains the barcode (16bp) and UMI (12bp) sequence, other sequence should be omitted. Though the sequencing is paired-end, but we only have one fastq file with valid sequence. I'm confused about the running command

• -u read2 --barcode read1 --UMI read1 --readFormat bc:0:15,um:16:27
• -1 read1 -2 read2 --barcode read1 --UMI read1 --readFormat bc:0:15,um:16:27,r1:28:-1

A snopshot of my fastq files

[Li Song]

In your case, since the other part in read1 is not useful, you shall use the first command "-u read2 --barcode read1 --UMI read1 --readFormat bc:0:15,um:16:27".

[Yunuuuu]

Thank you so much for your reply.