cloupe to 10x format

Question

[M'zelle]

Hello ! I have downloaded data from GEO bit there is not the 10X format (features.tsv, barcode.tsv, matrix.mtx), there is only cloupe file, is it possible to create the 10x format files from cloupe ? how can I do ? with R if possible please (I would like to create a seurat object) Thanks for you answers

Answer 1

[fracarb8]

As far as I know it should not be possible.

You can convert a seurat object to cloupe format, but not the inverse. This might change in the future (see here) . It is very strange that the authors uploaded in GEO only the cloupe file. Is the paper still in review? You should contact them and ask for the h5 files of the samples.

[M'zelle]

I am very new user so I do not know a lot, with just h5 file I can create this 10X format ? I thiink the h5 file is also available but I didn't figure out that it was possible to create my seurat object from this. Thanks a lot for your answer

[fracarb8]

If the h5 are available then you simply need to follow one the tutorials available on seurat's website. Based on the nature of the data and the type of analysis you are trying to do you should be able to find the right one, but if you don't know where to start, then pbmc 3k guided tutorial is a good start.

[GenoMax]

Which SRA# is this? If the original cellranger BAM files are available then you can recreate the fastq files using a utility that 10x provides.