# Failing to load single-cell raw fastq files into Galaxy

**URL:** <https://help.galaxyproject.org/t/failing-to-load-single-cell-raw-fastq-files-into-galaxy/6694>\
**Category:** usegalaxy.org support\
**Tags:** upload\
**Created:** [September 19, 2021, 2:51pm UTC](https://help.galaxyproject.org/t/failing-to-load-single-cell-raw-fastq-files-into-galaxy/6694 "2021-09-19T14:51:36Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![cathy37](https://avatars.discourse-cdn.com/v4/letter/c/e274bd/32.png) [@cathy37](https://help.galaxyproject.org/u/cathy37)\
**Post date:** [September 19, 2021, 2:51pm UTC](https://help.galaxyproject.org/t/failing-to-load-single-cell-raw-fastq-files-into-galaxy/6694/1 "2021-09-19T14:51:36Z")

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I am trying to use Faster Download and Extract Reads in FASTQ to download single-cell RNA-seq raw reads. The specific SRR accession is SRR11821880, and the SRA run browser tells me that there are three reads per spot. The first two are technical reads (adapter: 8 bp, barcode+UMI: 28 bp), and the last one is a biological read (150 bp).

My settings for the tool are:

- Select input type: SRR accession
- Advanced options\>Select how to split the spots: --split-files
- Advanced options\>Dump only biological reads: No

Currently, I am only getting the fastqs with the adapter sequences and the biological reads, but not the barcode+UMI. I’m unsure of why this is happening, since I am able to browse and view all of the reads in the run browser. Is this tool restricted to getting only two files maximum, or am I overlooking a setting?

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**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [September 20, 2021, 10:05am UTC](https://help.galaxyproject.org/t/failing-to-load-single-cell-raw-fastq-files-into-galaxy/6694/2 "2021-09-20T10:05:34Z")

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Hi @cathy37,  
it seems that is not possible to get the 3 reads at all, and the [ENA dump](https://www.ebi.ac.uk/ena/browser/view/SRR11821880?show=reads) also just contains 2 fastq files.

If you go to [https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11821880](https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11821880), under data access you can get the original files, that might be the easiest way to get them.

Regards