How to analyze single-cell ATAC-Seq data in R | Detailed Signac Workflow Tutorial

[@PsycheSnacks657]

The best KZbin channel to learn bioinformatics

[@jawad7776]

I can only wish to reach at the level of expertise you have...

[@aidaht1]

I really needed this😍thanks a lot❤️

[@samanwoymukherjee4945]

This is awesome Khusbu! As always 🎉 can you please cover Perturbseq and CiteSeq too

[@PoojaParishar]

This is one of the best tutorials I came across for scATACseq. Can you help me out with a problem. I am working with scATACseq data, but I am working with a non-standard organism (zebra finch). I looked for the genome for zebra finches on EnsDb and BSgenome, all of them have older assembly. I was able to find the new assembly files on UCSC and used it for reference genome cellranger-arc. Do you know any way of using the downloaded genome files for annotations and providing geneID for scATACseq?

[@mohammadyaghmoury1996]

another awesome tutorial. Keep up the good work.

[@arlenjamesmosqueraruiz957]

Nice tutorial. I have seen all of your videos and I have learned a lot! Thankss

[@vaviyanikunj7690]

hello maam, good video and is the best for the new transformations. i learned a lot but have one problem with the website of Vignette, metadata does not have any values in the column name "blacklist_region_fragments" so the analysis process is stopped midway for me. can you plz provide a link for metadata from your tutorial video?

[@nancyanderson5413]

Is there a chance of a tutorial for CUT&RUN or chip-seq soon?

[@wolveshowlhigh]

Do you have a tutorial for bulk ATACseq analysis?

[@SAMUTHIRAPANDISUBBURAJ]

It's really understandable and helpful for beginners in bioinformatics research like me. I request make class about data analysis for Copy Number Variation (CNV) and Structural Variation (SV)?.

[@johncruise6989]

Relevant question, If you do not have the `.h5` file, and have data that is formatted as three files, a counts file (`.mtx`), a cell barcodes file, and a peaks file. how should i laod the data and also what about fragments file ?

[@parnakanodia2262]

Hi thank you for your effort and attention to detail in creating these videos, could i please request you to see if you can post a lecture on "how to remove duplicates from fastq files using oxford academic's Bioinformatics' Minirmd 2021 tool(or anything else you feel would work better)? And kindly mention how/where in the RNAseq pipeline it would fit in heirarchy

[@yqh7297]

Could you make some videos about drug target mendelian randomization?

[@manushreesharma5793]

Hello Ma'am. Love your videos. I was hoping you could help me with a certain thing. So I had 5000+ protein sequences of a bacteria. I ran them on InterPro and obtained the tsv output. I obtained data such as GO annotations and pathway annotations. Now I need to find the function of these proteins. I am unable to figure out how to exactly proceed from here on. Could you please help me?

[@soumitadas6468]

Can you pls tell how to find promoter region in prokaryotic system?

[@sriyellampally2649]

can you make a video on GeoMx bulk RNA seq analysis workflow

[@oludelehalleluyah6723]

You're good. Please I want to learn bioinformatics very well. Can you give me list of textbooks I can read?

[@Po0pypoopy]

Chatgpt is pretty good at explaining things Just Google bioinformatics books and read some of them then ask ChatGPT to explain it further with examples

[@Wuhan.Huazhong]

can you make a sperate video tutorial on bulk ATAC-seq data analysis through linux operating system from very basics like to create environment and installation of software from where we can pick them up, and different file format. peak calling, differential accessible regions and if possible to integrate them with RNA-seq DEGs