Downloaded INVADEseq data not work for cellranger

[oyxf]

Dear author,

I encountered a problem when I used the released data from your work.

First, I downloaded the Invadeseq data from the SRA database, and used fastq-dump --split-files to convert the SRR file to fastq format. The final format was the same as the following picture:

Show Image

Second, I tried to analyze the data using cellranger, but the following error appeared:

Show Image

Could you please help me check if there was anything wrong with my process? Your help would be greatly appreciated!

Wish you the best in your research.

[sminot]

I'd be happy to provide some feedback on the possible causes of the error your encountered. Would you mind providing:

• The .nextflow.log file created by the run;
• The parameters, nextflow.config, and launch script that you used to start the run;
• Any other reference files which were used.

[hanruiw]

Dear oxyf,

Thank you very much for your interest in our work!

We understand that you encountered an issue while working with the dataset from our paper "Galeano Nino et al., Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer, 2022". To possibly remedy this, could you please attempt processing the 16s dataset once more using CellRanger version 6.1.1 and manually setting the chemistry to SC5P-PE? This adjustment might help in resolving the issue you are facing.

If you have any follow-up questions, please feel free to open a new issue here: Galeano Nino Bullman Intratumoral Microbiota 2022 GitHub Repository.

Thank you again for your engagement with our work, and we look forward to assisting you further.

Best regards, Hanrui