Hello everyone,
I am currently working on data organization and research related to perturb-seq, aiming to re-process upstream analyses using SRR files as input to generate the standard output files (features.tsv, barcodes.tsv, and matrix.mtx).
However, I have encountered a challenging technical issue. When using Cell Ranger to analyze FASTQ files, the pipeline requires a feature reference.csv file. Unfortunately, most datasets uploaded to the GEO database do not include this file, which prevents further analysis.
I downloaded h5ad files to obtain the "obs" and "var" information, but I still faced some problems: the formats of "obs" and "var" extracted from each h5ad file are inconsistent, and most databases do not even provide h5ad files. Are there any other ways to solve this problem?
I would appreciate any help.
Best regards, Rafe
What kind of technology is this data from? If it is Parse tech data then you may need to use their pipeline that you can get from here: https://support.parsebiosciences.com/hc/en-us/articles/27066395947412-How-Do-I-Analyze-my-Parse-Biosciences-Data