# Percentage Splice calculation using Galaxy

**URL:** https://help.galaxyproject.org/t/percentage-splice-calculation-using-galaxy/9224
**Category:** usegalaxy.org support
**Tags:** workflow, transcriptomics, featurecounts
**Created:** [December 26, 2022, 8:38pm UTC](https://help.galaxyproject.org/t/percentage-splice-calculation-using-galaxy/9224 "2022-12-26T20:38:11Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![Gavin\_Wang](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gavin_wang/32/2795_2.png) [@Gavin\_Wang](https://help.galaxyproject.org/u/Gavin_Wang)
#### Post date: [December 26, 2022, 8:38pm UTC](https://help.galaxyproject.org/t/percentage-splice-calculation-using-galaxy/9224/1 "2022-12-26T20:38:12Z")

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Hi Galaxy Community Galaxy, we mapped sequence reads from our RNA-Seq experiment to the S. Pome genome (see for your reference [Galaxy | Accessible History | Gavin project 2](https://usegalaxy.org/u/gavinwang/h/gavin-project-2)). We are trying to calculate splicing efficiency for all introns in S. pombe. I am seeking community help if anyone can guide me on how to obtain sequence reads for each intron and its flanking exons. Thank you in advance for the input and help !

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### Author: ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)
#### Post date: [January 3, 2023, 12:59am UTC](https://help.galaxyproject.org/t/percentage-splice-calculation-using-galaxy/9224/2 "2023-01-03T00:59:06Z")

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Hi @Gavin_Wang  
maybe follow any published protocol/workflow. If you are after read counts in exons, maybe look at DEXSeq tools or use tools like featureCounts without aggregation of counts. To get sequences have a look at interval tools, such as bedtools. You also can get positions of introns using bedtools, if you have 12 columns BED files.  
Kind regards,  
Igor