Question

What are R1, R2, R3, and I1 in a illumina sequencing data, and how can I get more information about them?

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2.2 years ago

Vijith ▴ 90

I am a fresher in Bioinformatics, especially in NGS. As of now, I am working on a WGS project, and the sequence read data include R1, R2, R3, and I1. I have understood that I1 is the index file, and based on query with someone I was told that R2 is barcode data. Can someone help me how we can delineate those information about the read files?

illumna NGS generation sequencing next • 3.2k views

ADD COMMENT • link updated 2.2 years ago by Prash ▴ 280 • written 2.2 years ago by Vijith ▴ 90

score 3 · Answer 1 · 2022-09-29

Are you sure this is a WGS project? In general these kind of data files are produced as a part of multiome 10x single-cell ATAC 10x projects produced by cellranger-arc mkfastq software. They are then used with cellranger-arc count.

I1: Dual index i7 read 
R1: Read 1
R2: Dual index i5 read
R3: Read 2

score 1 · Answer 2 · 2022-09-29

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2.2 years ago

Prash ▴ 280

I agree with GenoMax And even for natepairs, these are NOT the labeling used. I is certainly the index case. Can you please provide the screenshot of files?

ADD COMMENT • link 2.2 years ago by Prash ▴ 280

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ADD REPLY • link 2.2 years ago by Vijith ▴ 90

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:-) I was expecting the file sizes. sorry

ADD REPLY • link 2.2 years ago by Prash ▴ 280