# Pre-processing of Single-Cell RNA Data Tutorial Troubleshooting
**URL:** https://help.galaxyproject.org/t/pre-processing-of-single-cell-rna-data-tutorial-troubleshooting/8180
**Category:** Uncategorized
**Tags:** troubleshooting, single-cell
**Created:** [June 9, 2022, 4:01pm UTC](https://help.galaxyproject.org/t/pre-processing-of-single-cell-rna-data-tutorial-troubleshooting/8180 "2022-06-09T16:01:01Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@swren](https://help.galaxyproject.org/u/swren)
#### Post date: [June 9, 2022, 4:01pm UTC](https://help.galaxyproject.org/t/pre-processing-of-single-cell-rna-data-tutorial-troubleshooting/8180/1 "2022-06-09T16:01:01Z")
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.
---
### Author:  [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)
#### Post date: [June 9, 2022, 6:25pm UTC](https://help.galaxyproject.org/t/pre-processing-of-single-cell-rna-data-tutorial-troubleshooting/8180/2 "2022-06-09T18:25:02Z")
Hi @swren,
I contacted the people who developed the training; probably they will provide you an answer in a few days.
Best regards!
---
### Author:  [@mtekman](https://help.galaxyproject.org/u/mtekman)
#### Post date: [June 10, 2022, 9:25pm UTC](https://help.galaxyproject.org/t/pre-processing-of-single-cell-rna-data-tutorial-troubleshooting/8180/3 "2022-06-10T21:25:15Z")
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.
---
### Author:  [@swren](https://help.galaxyproject.org/u/swren)
#### Post date: [June 14, 2022, 2:37pm UTC](https://help.galaxyproject.org/t/pre-processing-of-single-cell-rna-data-tutorial-troubleshooting/8180/4 "2022-06-14T14:37:34Z")
Hi @mtekman, thank you for reaching out! Here is the link to my history: [Galaxy | Europe | Accessible History | Preprocessing of scRNA Data](https://usegalaxy.eu/u/spencer/h/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!
---
### Author:  [@mtekman](https://help.galaxyproject.org/u/mtekman)
#### Post date: [June 30, 2022, 1:38pm UTC](https://help.galaxyproject.org/t/pre-processing-of-single-cell-rna-data-tutorial-troubleshooting/8180/5 "2022-06-30T13:38:39Z")
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:
```auto
https://zenodo.org/record/3253142/files/SRR5683689_1.fastq
https://zenodo.org/record/3253142/files/SRR5683689_2.fastq
```
(note the lack of “\_subset” prefix)
---
### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [July 23, 2022, 12:52am UTC](https://help.galaxyproject.org/t/pre-processing-of-single-cell-rna-data-tutorial-troubleshooting/8180/6 "2022-07-23T00:52:33Z")