Deduplicate reads from 10x fragment.tsv.gz

[vikon72]

hi ,there
I found that there was no dedup in the 10x fragment file. It includes the read pair marked unique and all duplicate read pairs. Whether it leads to calculations of gene scores exists error?

[rcorces]

I'm afraid your interpretation of the fragment file is incorrect.
https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments
The 4th column is
"The total number of read pairs associated with this fragment. This includes the read pair marked unique and all duplicate read pairs"

[vikon72]

hi,
Thanks for your reply.But In my sight，it just means Total read pais includes all reads pairs,How do you understand that?
In addition，this is a part of my 10X fragment file.It was acquired by cellranger-atac 2.1.0.The same cut sites appears more than once.
It was changed a lot between cellranger-atac 1.1.0 and cellranger-atac 2.1.0.Some functions In ArchR maybe effective no longer.such as
- getValidBarcodes(). Is there an update plan？

chr1 181470 181519 AATGCCATCGAGAAGC-1 2
chr1 181470 181519 ACCAAACGTGCCCTAG-1 4
chr1 181470 181519 CAATCCCCAAGTTGCT-1 2
chr1 181470 181519 CACCTTGGTATTGTCG-1 2
chr1 181470 181519 TAGTCCCTCTCCCTTT-1 1
chr1 181470 181520 AAATGAGAGTACCACT-1 2
chr1 181470 181520 ACCGCAGTCACGTCAA-1 1
chr1 181470 181520 CAGTATGAGCATACCT-1 1
chr1 181470 181521 AAATGCCGTATTCACG-1 1
chr1 181470 181521 ACATGGTGTATTCACG-1 5
chr1 181470 181521 ATTTGTCGTCTGGTTA-1 3
chr1 181470 181521 CCGTACTTCTGCCGAG-1 1
chr1 181470 181521 CTCTACGGTGATCAGG-1 3
chr1 181470 181521 TCAATTCAGCCCATGC-1 3
chr1 181470 181521 TGCATGATCGCGTTCT-1 2

Thanks!