-
Hi,
I understand that the default mapping option for the ATAC-seq data is pair ended, but is there a mapping option for a single ended ATAC-seq data?
Thank you,
Lindsay
-
Hello,
I am trying to run the pipeline for chicken samples and have tried to create a custom genome reference for the pipeline. However, after finishing the steps here [https://github.com/ENCODE-de…
-
helper script to map features to genomic regions as BED files (code exists)
Add all mentioned helper scripts to the respective recipes and link from the main repository to the recipe so it’s always i…
-
Hallo all,
I was reading the pepatac publication and I read a bit their pipeline. I find it to be the most interesting and comlete pipeline for ATAC.
Since it is very tough to get the whole pipeline…
-
Dear,
Is it possible to use EPIC for cell type deconvolution using ATAC-seq datasets?
It gives the following error when I provide bulk ATAC-seq matrix (rows=peaks, columns=sample/subject) as inp…
-
I am trying to call peaks in ATAC-seq data. According to the documentation:
> To find enriched cutting sites such as some DNAse-Seq datasets. In this case, all 5' ends of sequenced reads should be ex…
-
Hi,
I have gone through the other two ATAC-seq issues. Accordingly, I tried one run with BAMPE and one without. here are the codes.
``macs2 callpeak -t raw/dH1f_1.bam -n dh1f_1.broad -g hs -q 0.05…
-
Hello,
I'm interested in using scglue to integrate my scRNAseq with scATACseq data, comprising four paired samples. These datasets are not multiome; they're only paired samples.
After processing…
-
Hi, I have some unpaired scRNA-seq and scATAC-seq data, they are sequencing the same samples, but in separate scRNA-seq and scATAC-seq assays, so the cell barcodes are different in these datasets. How…
-
Hi,
Could you maybe add an explanation of what exactly the ATACseq mode (-A flag) is doing differently to DNase mode? Also should the input BAMs for ATACseq mode be Tn5 shifted or not?
Thanks