#ATACseq

Pierre Lindenbaumyokofakun@genomic.social
2024-08-08

I wrote my notes for using #nfcore /differencialabundance with the output of nfcore/atacseq" in the following gist: gist.github.com/lindenb/593ad9

#nextflow #atacseq

James Hawley, PhDjrhawley@scholar.social
2023-12-04

For scRNA-seq and scATAC-seq, have people been using "reads" as the important measurement instead of "fragments" for the past few years? Because this paper seems to suggest people have been unintentionally over-inflating the variance in their data by counting "reads"

nature.com/articles/s41592-023

I thought we we figured this out a long time ago with the whole "RPKM vs FPKM vs TPM" debate in bulk RNA-seq years ago.

#single_cell #rnaseq #atacseq #compBio #bioinformatics

Alberto Perez-Posadaapposada@genomic.social
2023-06-29

serious question. When one runs motif enrichment analysis, I think it is generaly desirable to know which specific peaks were found to have a motif. Why does a tool like HOMER's FindMotifsGenome.pl not report every instance of where each motif was found, and one must run a whole different tool for that task? Is this a feature more people would wish for?

#genomics #bioinformatics #atacseq #chromatin #motifs #computational #compbiology

2023-03-19

Anyone know a good review paper / learning resource for building gene regulatory networks #GRN from #scATACseq #ATACseq and/or #scRNAseq data?
Thanks!

2022-12-28

This useful paper looks into strengths and weaknesses of #TnSeq approaches in #bacterial #genetics screens for essential genes.

Importantly, a lot of false positives are attributable to Tn insertion failure on nucleoid-associated DNA — a result that my friends who use #ATACSeq & similar methods to map chromatin states in eukaryotes will be unsurprised by.

The obvious workaround is in vitro transposition on isolated DNA, if your system is amenable to that approach.

journals.asm.org/doi/full/10.1

Human fetal lung single cell atlas. scRNA-seq + scATAC-seq + Visium combined. Key finding: unrecognized cell states such as new progenitors and a subset of neuroendocrine cell related to lung cancer.
#singlecell #cellatlas #atacseq #spatialtranscriptomics #devbio
cell.com/cell/fulltext/S0092-8

2022-12-10

And finally, some skills that will be helpful: #bioinformatic and #statistical skills: population genetics/#genomics, quantitative genetics, #RNAseq, #ATACseq, integration of #multi_omics data; willingness to get involved in data generation (wet lab) is a plus.

2022-10-28

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