Could you please provide some intermediate files so people like me can go through the whole classes?

[zzygyx9119]

I was wondering whether you could provide the intermediate files used as examples in this amazing tutorial.

I downloaded some files, such as "ERR522959_2.fastq", "ERR522959_1.fastq", to follow along the class, but couldn't find the files like "data/10cells_read1.fq, data/10cells_read2.fq", "data/droplet_id_example_per_barcode.txt.gz", "data/droplet_id_example_truth.gz".

I had experience in analyzing bulk RNAseq data, and is not currently working on ScRNAseq data. For some reasons, it is impractical for me to download all the original fastq files to our server to generate all the intermediate files. What I hope to do is to be able to follow along your classes on my personal Mac computer to get familiar with all the tools and the workflow of ScRNAseq analysis.

So I would greatly appreciate your kindness to provide a link (either here or some other sources) to download the intermediate files required to work through the examples in this class.

Best,

Jeff

[matrs]

Hi, droplet_id_example_truth.gz and droplet_id_example_per_barcode.txt.gz are available here: https://scrnaseq-course.cog.sanger.ac.uk/index.html?prefix=data/

I was looking for the "10cells" fastqs but as far as I can tell they aren't vailable.

[xloctran]

I think these files you are looking for can be generated from the file EXAMPLE.cram by converting it into fastq file using bedtools as indicated in the tutorial.