Does latf-load not support single-cell RNA-seq data, including index files?

[chunryongoh]

Hi,

I am currently trying to convert 10x Genomics single-cell RNA-seq data into .sra format using latf-load, but I'm encountering issues when the dataset contains multiple FASTQ files (e.g., R1, R2, and I1 for the index). It seems that latf-load cannot handle more than two FASTQ files per sample, which results in a "duplicate read name" error when processing single-cell RNA-seq datasets that include index reads (e.g., I1).

I would like to ask a few questions to clarify the current status and limitations of latf-load:

Does latf-load officially support 10x single-cell RNA-seq datasets, particularly those with index files (e.g., I1)?

Is there an alternative recommended method or pipeline (perhaps XML-based like fastq-load or a newer internal system) that NCBI uses for ingesting such datasets?

Is latf-load still being actively maintained, or has it been deprecated in favor of other tools?

I appreciate any guidance on how to properly load and submit these types of single-cell datasets to SRA.

Thank you in advance for your help!

Best regards,
Chunryong

[durbrow]

If your intention is to submit the files to SRA, you do not need to load them first. Please email sra@ncbi.nlm.nih.gov if you need help submitting your files to the archive.

[chunryongoh]

Thank you for the clarification.

Just to add — I’m not looking to submit data at the moment. I'm simply curious about how different types of sequencing data, especially 10x single-cell RNA-seq with index reads, are converted into .sra format.

I’m particularly interested in whether latf-load supports multi-FASTQ input (e.g., R1, R2, I1), and if not, what tools or pipelines (like fastq-load or others) are typically used at NCBI for such cases.

Any information or documentation would be greatly appreciated.