DEseq analysis on featurecounts from two chromosomes of the same genome

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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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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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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

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