# Demultiplexing and Quantification of 10X Single-Cell RNA-Seq Datasets using rna star solo

**URL:** <https://help.galaxyproject.org/t/demultiplexing-and-quantification-of-10x-single-cell-rna-seq-datasets-using-rna-star-solo/9394>\
**Category:** usegalaxy.org support\
**Tags:** troubleshooting, single-cell\
**Created:** [February 2, 2023, 8:35am UTC](https://help.galaxyproject.org/t/demultiplexing-and-quantification-of-10x-single-cell-rna-seq-datasets-using-rna-star-solo/9394 "2023-02-02T08:35:37Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![aa\_mm](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/aa_mm/32/3974_2.png) [@aa\_mm](https://help.galaxyproject.org/u/aa_mm)\
**Post date:** [February 2, 2023, 8:35am UTC](https://help.galaxyproject.org/t/demultiplexing-and-quantification-of-10x-single-cell-rna-seq-datasets-using-rna-star-solo/9394/1 "2023-02-02T08:35:37Z")

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I have two fastq reads (R1 and R2) for single cell rna-seq data.  
R1 is 9.5GB and R2 is 19.5 GB. As far as I know R1 is usually the barcode read and R2 is the cDNA read.  
I am trying to follow the galaxy pipeline [Hands-on: Hands-on: Pre-processing of 10X Single-Cell RNA Datasets / Single Cell](https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html)

But in this training 4 files are used, two files for each reads. I only have two files, one file per read. I used R1 as barcode read and R2 as cDNA read as the input parameters for rna star solo. But I got an error in generating alignment bam file and all the other files were empty.

Can anyone help me figure out? I am new to this whole thing.

Thanks

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [March 10, 2023, 8:10pm UTC](https://help.galaxyproject.org/t/demultiplexing-and-quantification-of-10x-single-cell-rna-seq-datasets-using-rna-star-solo/9394/2 "2023-03-10T20:10:08Z")

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Resolved in reruns.

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [March 10, 2023, 8:10pm UTC](https://help.galaxyproject.org/t/demultiplexing-and-quantification-of-10x-single-cell-rna-seq-datasets-using-rna-star-solo/9394/3 "2023-03-10T20:10:17Z")

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Closed on March 10, 2023, 8:10pm UTC