# How can I find that a RNAseq data is stranded or un-stranded by usegalaxy tools?

**URL:** <https://help.galaxyproject.org/t/how-can-i-find-that-a-rnaseq-data-is-stranded-or-un-stranded-by-usegalaxy-tools/4832>\
**Category:** usegalaxy.eu support\
**Tags:** gtn-tutorial, mapping\
**Created:** [November 13, 2020, 9:47am UTC](https://help.galaxyproject.org/t/how-can-i-find-that-a-rnaseq-data-is-stranded-or-un-stranded-by-usegalaxy-tools/4832 "2020-11-13T09:47:46Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![sajjadg4](https://avatars.discourse-cdn.com/v4/letter/s/59ef9b/32.png) [@sajjadg4](https://help.galaxyproject.org/u/sajjadg4)\
**Post date:** [November 13, 2020, 9:47am UTC](https://help.galaxyproject.org/t/how-can-i-find-that-a-rnaseq-data-is-stranded-or-un-stranded-by-usegalaxy-tools/4832/1 "2020-11-13T09:47:46Z")

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Hi . Im looking into a package in usegalaxy that can show my RNAseq data is stranded or unstranded.

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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:** [November 14, 2020, 9:27am UTC](https://help.galaxyproject.org/t/how-can-i-find-that-a-rnaseq-data-is-stranded-or-un-stranded-by-usegalaxy-tools/4832/2 "2020-11-14T09:27:22Z")

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Hi @sajjadg4,  
in order to know if your RNAseq datasets are stranded or unstranded, you need to align it against the reference genome; you can use RNA STAR. Then by using the BAM/SAM Mapping Stats tool, you can infer it by comparing the number of reads which map to positive and negative strand.

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**Author:** ![labnv40](https://avatars.discourse-cdn.com/v4/letter/l/5daacb/32.png) [@labnv40](https://help.galaxyproject.org/u/labnv40)\
**Post date:** [November 17, 2020, 12:25pm UTC](https://help.galaxyproject.org/t/how-can-i-find-that-a-rnaseq-data-is-stranded-or-un-stranded-by-usegalaxy-tools/4832/3 "2020-11-17T12:25:23Z")

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Hi @sajjadg4,

after mapping, you can check strandness using the “Infer Experiment” function of the RSeQC package.

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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:** [November 17, 2020, 10:34pm UTC](https://help.galaxyproject.org/t/how-can-i-find-that-a-rnaseq-data-is-stranded-or-un-stranded-by-usegalaxy-tools/4832/4 "2020-11-17T22:34:52Z")

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GTN tutorial help for determining strandedness. Even if putatively “known”, it is a good idea to check.

> **[Galaxy Training: RNA-Seq reads to counts](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html#strandness)**
>
> Training material for all kinds of transcriptomics analysis.

> **[Galaxy Training: De novo transcriptome reconstruction with RNA-Seq](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/de-novo/tutorial.html#mapping)**
>
> Training material for all kinds of transcriptomics analysis.