Pre-processing of Single-Cell RNA Data Tutorial Troubleshooting

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I have worked through the Single-Batch Processing hand-on tutorial three times and consistently get different results than what the tutorial says. After the UMI-tool count (last step of the Single-Batch Processing), the tutorial states there should be 2,140 lines in the matrix and 180 columns, but I am consistently getting 1,972 lines and 50 columns.

Is anyone else experiencing this?

Does anyone have any ideas why this is happening? I made sure to use the Tutorial Mode on galaxy, so when I would select the next step it took me to the appropriate tool and version.

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Hi @swren,
I contacted the people who developed the training; probably they will provide you an answer in a few days.

Best regards!

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Hi @swren, thanks for trying out the training, could you share your history with me so that I might be able to debug it? My user-name is “mehmet-tekman”

I will be out of office for a few days, but will happily look at your history when I am back.

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Hi @mtekman, thank you for reaching out! Here is the link to my history: Galaxy | Europe | Accessible History | Preprocessing of scRNA Data

I have two tries on this history, and the second try is the one that I used tutorial mode for the links to the tools.

Thank you!

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Dear @swren - I am back from holiday, thanks for sharing your history.

Can you try the analysis again, this time using slightly different input FASTQ files:

https://zenodo.org/record/3253142/files/SRR5683689_1.fastq
https://zenodo.org/record/3253142/files/SRR5683689_2.fastq

(note the lack of “_subset” prefix)

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