Upstream related to perturb-seq
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Rafe Wang
Jul 15, 2025, 11:13:26 PM7/15/25
to Perturb-seq
Hello everyone,
I currently re-process upstream analyses using SRR files as input to generate the standard output files (features.tsv, barcodes.tsv, and matrix.mtx).
I used cell ranger to analyze FASTQ files, the pipeline requires a feature reference.csv file. But most datasets don't have this file.
I would like to inquire：Did you face a similar challenge in your study? If so, could you share how this issue was resolved?
I have downloaded h5ad files to obtain "obs" and "var" information, but there are still some problem: the formats of "obs" and "var" extracted from each h5ad file are inconsistent, and most databases do not even provide h5ad files.
Many thanks for your help!
Best,
Rafe
I currently re-process upstream analyses using SRR files as input to generate the standard output files (features.tsv, barcodes.tsv, and matrix.mtx).
I used cell ranger to analyze FASTQ files, the pipeline requires a feature reference.csv file. But most datasets don't have this file.
I would like to inquire：Did you face a similar challenge in your study? If so, could you share how this issue was resolved?
I have downloaded h5ad files to obtain "obs" and "var" information, but there are still some problem: the formats of "obs" and "var" extracted from each h5ad file are inconsistent, and most databases do not even provide h5ad files.
Many thanks for your help!
Best,
Rafe
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