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

chatomics
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30 окт 2024

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Комментарии : 15   
@fp2551
@fp2551 5 месяцев назад
Thank you, this was very helpful! Appreciate your clear explanation :)
@chatomics
@chatomics 5 месяцев назад
You are welcome!
@AC-cz6rv
@AC-cz6rv Год назад
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
@chatomics Год назад
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
@AC-cz6rv Год назад
@@chatomics Thank you so much. I am very grateful and appreciative.
@HafeezUrRehman-s2h
@HafeezUrRehman-s2h 5 месяцев назад
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
@chatomics 5 месяцев назад
People deposit data in GEO with different formats. Which one are you taking about?
@jshn93
@jshn93 Год назад
Thank you for the great and informative video! I am curious if this methodology can be applied to bulk RNAseq data as well.
@chatomics
@chatomics Год назад
Yes, for bulk RNAseq use pachterlab.github.io/kallisto/starting
@jshn93
@jshn93 Год назад
@@chatomics Thank you!
@AnimeshSharma1977
@AnimeshSharma1977 Год назад
Thanks for sharing 👍Wondering if it is respecting the paired-end-reads information or treat them as unpaired?
@chatomics
@chatomics Год назад
It should respecting the paired-end
@shrithikag4907
@shrithikag4907 10 месяцев назад
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
@chatomics 10 месяцев назад
take a look at salmon.readthedocs.io/en/latest/salmon.html#quantifying-in-alignment-based-mode
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