How to Process Single Cell RNAseq with 2 lines of code from fastq to count matrix 🧬

[@AC-cz6rv]

Dear Tom , very cool and easy to understand and learn tutorials! Thank you so much for your generosity . Might you be willing to make a video to explain how one can customize the ref genome /annotation e.g. adding a GFP or focusing on specific chromosome or reducing the analysis to mitochondrial transcripts? there are no videos that teach such a valuable skill!

[@chatomics]

You will need to make a fasta file with GFP sequence, and create a GTF file. I did something like this: divingintogeneticsandgenomics.com/post/cellranger-mk-reference-with-transgenes/

[@AC-cz6rv]

@@chatomics Thank you so much. I am very grateful and appreciative.

[@fp2551]

Thank you, this was very helpful! Appreciate your clear explanation :)

[@chatomics]

You are welcome!

[@HafeezUrRehman-s2h]

Hello Tom, thanks for such a wonderful tutorial. Currently, i have worked how to do the single cell RNA-Seq starting from the .hf file format from 10x genomics. i do not know how to retrieve the data from GEO Datasets for single cell rna seq analysis and to which file format we will convert this data first for scRNA-Sed analysis

[@chatomics]

People deposit data in GEO with different formats. Which one are you taking about?

[@jshn93]

Thank you for the great and informative video! I am curious if this methodology can be applied to bulk RNAseq data as well.

[@chatomics]

Yes, for bulk RNAseq use pachterlab.github.io/kallisto/starting

[@jshn93]

@@chatomics Thank you!

[@AnimeshSharma1977]

Thanks for sharing 👍Wondering if it is respecting the paired-end-reads information or treat them as unpaired?

[@chatomics]

It should respecting the paired-end

[@shrithikag4907]

I have a bam file and i want a get a count matrix file , i covereted my bam to fastq but spliting of the fastq file is not happing correctly.

[@chatomics]

take a look at salmon.readthedocs.io/en/latest/salmon.html#quantifying-in-alignment-based-mode