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!
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/
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
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!
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/
@@chatomics Thank you so much. I am very grateful and appreciative.
Thank you, this was very helpful! Appreciate your clear explanation :)
You are welcome!
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
People deposit data in GEO with different formats. Which one are you taking about?
Thanks for sharing 👍Wondering if it is respecting the paired-end-reads information or treat them as unpaired?
It should respecting the paired-end
Thank you for the great and informative video! I am curious if this methodology can be applied to bulk RNAseq data as well.
Yes, for bulk RNAseq use pachterlab.github.io/kallisto/starting
@@chatomics Thank you!
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.
take a look at salmon.readthedocs.io/en/latest/salmon.html#quantifying-in-alignment-based-mode