# DEseq analysis on featurecounts from two chromosomes of the same genome

**URL:** <https://help.galaxyproject.org/t/deseq-analysis-on-featurecounts-from-two-chromosomes-of-the-same-genome/15528>\
**Category:** Uncategorized\
**Tags:** transcriptomics\
**Created:** [May 24, 2025, 3:19pm UTC](https://help.galaxyproject.org/t/deseq-analysis-on-featurecounts-from-two-chromosomes-of-the-same-genome/15528 "2025-05-24T15:19:07Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ATIKAKO\_KOSSIVI](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/atikako_kossivi/32/6083_2.png) [@ATIKAKO\_KOSSIVI](https://help.galaxyproject.org/u/ATIKAKO_KOSSIVI)\
**Post date:** [May 24, 2025, 3:19pm UTC](https://help.galaxyproject.org/t/deseq-analysis-on-featurecounts-from-two-chromosomes-of-the-same-genome/15528/1 "2025-05-24T15:19:07Z")

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Hello,  
I am new in bioinformatic analysis and I am performing TnSeq analysis which work well. My bacteria has two chromosomes, so I performed all my analysis separately on each chromosome so I got featurecounts for each chromosome and I would like to run DEseq. My question is that should I run the DEseq also for each chromosome or should I combine the featurecounts from both chromosomes for DEsq.  
Thanks

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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:** [May 27, 2025, 1:19am UTC](https://help.galaxyproject.org/t/deseq-analysis-on-featurecounts-from-two-chromosomes-of-the-same-genome/15528/2 "2025-05-27T01:19:44Z")

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Hi @ATIKAKO_KOSSIVI,

Usually, gene annotations cover the whole genome. I am not sure how you got separate tables for chromosomes. For example, we get a single table with read counts for human genome.

I recommend doing gene expression analysis on the whole genome. You probably can combine counts (number of reads mapped to genes), but not normalized counts. A better option is an annotation for the whole genome for read counting step.

Kind regards,  
Igor

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<div class="post-metadata">

**Author:** ![ATIKAKO\_KOSSIVI](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/atikako_kossivi/32/6083_2.png) [@ATIKAKO\_KOSSIVI](https://help.galaxyproject.org/u/ATIKAKO_KOSSIVI)\
**Post date:** [May 27, 2025, 6:41pm UTC](https://help.galaxyproject.org/t/deseq-analysis-on-featurecounts-from-two-chromosomes-of-the-same-genome/15528/3 "2025-05-27T18:41:56Z")

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Thank you for your fast reply, you are right, I run again the read count this time using the whole genome and that solve my issue.

Thanks again