# RNA-seq reads to counts with pair-end data

**URL:** <https://help.galaxyproject.org/t/rna-seq-reads-to-counts-with-pair-end-data/9526>\
**Category:** usegalaxy.eu support\
**Tags:** workflow\
**Created:** [February 28, 2023, 2:31pm UTC](https://help.galaxyproject.org/t/rna-seq-reads-to-counts-with-pair-end-data/9526 "2023-02-28T14:31:48Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![omer\_p](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/omer_p/32/4028_2.png) [@omer\_p](https://help.galaxyproject.org/u/omer_p)\
**Post date:** [February 28, 2023, 2:31pm UTC](https://help.galaxyproject.org/t/rna-seq-reads-to-counts-with-pair-end-data/9526/1 "2023-02-28T14:31:48Z")

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Hello,  
I’m trying to follow the tutorial of RNA-seq reads to counts, I have pair-end data from ENA but the tutorial reffers only to single pair data. I tried to follow the training whithout buliding a collection. I trimed the reads with Trim Galore instead of Cutadapt. when I wanted to proceed with fastQC I couldn’t understand which files of my rawdata I should choose.

I’d apricceate your help with analyzing paird-end data.

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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:** [February 28, 2023, 3:02pm UTC](https://help.galaxyproject.org/t/rna-seq-reads-to-counts-with-pair-end-data/9526/2 "2023-02-28T15:02:51Z")

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Hi @omer_p,  
currently FASTQC doesn’t accept pared-end reads as input; you can combine the trimmed reads pair 1 and trimmed reads pair 2 files in a single file (for example by using [concatenate datasets](https://usegalaxy.eu/root?tool_id=cat1) and the use it as input for FASTQC.

Regards