Cell Ranger - Process 10x genomics data (Part1)

In this video we explore cellranger tool which is used to process 10x genomics data. We explore its algorithm, different commands of it. This video is mainly theory. In Part2 we will do hands on.

[@gerardhoeltzel4690]

youre goated

[@2007dolphinlover]

What is the citation/paper at 1:37. Excellent diagram!

[@bioinfquests]

If I am not wrong it's www.nature.com/articles/s41596-018-0073-y Is this video useful? Any positive or negative feedback would be valuable.

[@2007dolphinlover]

@@bioinfquests Yes, this video is very useful! I keep coming back to it. :D THANK YOU!!

[@AnkitYadav-v2v8z]

I want to do this on my own data beause we have our own sequencing machice and we do the sequencing inhouse so is it possible to genrate a counts data using cellranger

[@bioinfquests]

Yes cell ranger pipeline starts from fastq to count. U can refer the 2nd part of this video to know more.

[@AnkitYadav-v2v8z]

​@@bioinfquestsI am reaching out to inquire about Cell Ranger and its compatibility with our in-house sequencing setup. We currently have our own sequencer and would like to explore the possibility of using Cell Ranger to generate counts from our own BCL data. As I have limited hands-on exposure in library preparation, I wanted to understand if any modifications or changes are required in the library preparation process to use Cell Ranger effectively. Could you please provide some insights into how Cell Ranger works and whether it can be seamlessly integrated with our existing library preparation workflow?

[@thuongpham8912]

It's super useful! I was looking for some information like this since I'm more a computing side but is doing collaboration with people using 10X, which I have not much knowledge about. Thank you so much for your work!

[@5602KK]

I feel like this is an excellent video but I can barely hear you man

[@King_of_carrot_flowers]

Excellent tutorial. I appreciate you showing how samples are set up on the chip.

[@bioinfquests]

Glad it was helpful!