how could I select low 'fraction fragments overlapping peaks' but 'high fragments per barcode' in scATAC-seq analysis?
0
0
Entering edit mode
23 months ago
Chilly ▴ 10

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 • 802 views
ADD COMMENT

Login before adding your answer.

Traffic: 2713 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6