Cutoffs and Thresholds for single nuclei and single cell RNAseq data

 

paper : https://www.biorxiv.org/content/biorxiv/early/2021/06/25/2021.06.25.449944.full.pdf

Data Downloads with SFTP Commands

sftp> lpwd

Local working directory: /home/user/

sftp> lcd /home/user/Data/

sftp> lpwd

Local working directory: /home/user/Data/

for d in abc842  abc9829 abc8424; do var=`echo $d | sed 's/abc/Sample_ABC/g'`; echo "get -R $var"; done

get -R Sample_ABC8425

get -R Sample_ABC9829

get -R Sample_ABC8424

paste the above get-R commands in the sftp command prompt to download the data to server

Resolved: Error: object ‘LayerData<-’ is not exported by 'namespace:SeuratObject'

Signac gives me :

Error: object ‘LayerData<-’ is not exported by 'namespace:SeuratObject'

Execution halted

I updated my SeuratObject (4.1.3     -> 5.0.0    ) [CRAN]

Notes on snapatac2

When I ran:

data = snap.pp.import_data(

    fragment_file,

    chrom_sizes=snap.genome.hg38,

    #file="2_filtered_data/ATAC/atac_test.h5ad",  # Optional

    sorted_by_barcode=False,)

------------------------

fragment_file being fragments.tsv.gz and fragments.tsv generated the error

PanicException: called `Result::unwrap()` on an `Err` value: Custom { kind: Other, error: "Unknown frame descriptor" }

instead i used fragments.srt.bed.gz generated from :

time sort -k4,4 fragments.tsv | gzip - > fragments.srt.bed.gz,

resolved the issue