how could I select low 'fraction fragments overlapping peaks' but 'high fragments per barcode' in scATAC-seq analysis?
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2.5 years ago
Chilly ★ 1.3k

I am doing a single cell ATAC-seq analysis. My data was generated using the 10x kit. Shown in the attachment is a part of the report generated by the 'cellranger-atac count' pipeline of the 10x.

enter image description here Below is my command to run the pipeline

cellranger-atac count --id=ATAC_2 --fastqs=~/ATAC_2/ --sample=ATAC_2 --reference=~/hrs1p0_primary --chemistry=ARC-v1

In above picture, yellow dots represent the 'cell' selected by the pipeline, and blue represents unselected. However, I think the part circled by the red line in the image below is the data I'm interested in: enter image description here

So I did the 'force cell' number:

cellranger-atac count --id=ATAC_2_1500 --fastqs=~/ATAC_2/ --sample=ATAC_2 --reference=~/hrs1p0_primary --chemistry=ARC-v1 --force-cells=1500

The selection of cells was forced to increase, but not as much as I needed: enter image description here

How could I select low 'fraction fragments overlapping peaks' but 'high fragments per barcode' in scATAC-seq analysis? In the pipeline manualenter link description here, there are no more options to set. Is there any other way or tool?

Thank you for your attention!

cellranger ATAC-seq peak ATAC 10x • 939 views
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