Entering edit mode
20 hours ago
Pallondyle
•
0
I'm running a scATAC-seq analysis. The data was obtained from the published work: Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers; https://ngdc.cncb.ac.cn/omix/; OMIX005759; OMIX005759-04.sort.fragments.tsv.gz.
However, when I run the following code, I call these peaks:
peaks2 <- CallPeaks(frags2,macs2.path="/home/anaconda3/envs/lowpython/bin/macs2",combine.peaks=F)
peaks2@ranges
#IRanges object with 24 ranges and 0 metadata columns:
# start end width
# <integer> <integer> <integer>
# [1] 9968 248946051 248936084
# [2] 10191 133787023 133776833
# [3] 146452 135076001 134929550
# [4] 15323 133236135 133220813
# [5] 18172397 114353789 96181393
# ... ... ... ...
# [20] 19503 159335730 159316228
# [21] 82336 145075845 144993510
# [22] 10409 138233182 138222774
# [23] 2781347 156030667 153249321
# [24] 268144 57217121 56948978
They are obviously too wide to be "peaks"! My complete code is as follows:
## PATH
fragpath2 <- "/data/Tide/rawdata/TangLab-scATAC-seq/OMIX005759-04.sort.fragments.tsv.gz"
## require essential informations
total_counts <- CountFragments(fragpath)
cutoff <- 1000 # Change this number depending on your dataset!
barcodes <- total_counts[total_counts$frequency_count > cutoff, ]$CB
## create .tbi index
gunzip rawdata/TangLab-scATAC-seq/OMIX005759-04.sort.fragments.tsv.gz
bgzip rawdata/TangLab-scATAC-seq/OMIX005759-04.sort.fragments.tsv
tabix -p bed rawdata/TangLab-scATAC-seq/OMIX005759-04.sort.fragments.tsv.gz
## Create fragment object
frags2 <- CreateFragmentObject(path = fragpath2, cells = barcodes)
## peak calling
peaks2 <- CallPeaks(frags2,macs2.path="/home/anaconda3/envs/lowpython/bin/macs2")
The version of RStudio: 4.3.1 The version of Signac: 1.14.0 The version of MACS2: 2.1.4 How could I fix this problem?
