Bacterial metatranscriptomics with DESEQ2?

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2.9 years ago

shail.nair05 ▴ 20

HI, I want to compare the differential expression (prokaryotic) in metatranscriptomics samlples form two different conditions. I used Prodigal to get the gff file and later used featurecount to get the raw counts of each predicted region. But from some of the blogs/articles it is mentioned that for Differential expression analysis we should use Exon count rather than CDS. Prodigal can predict just CDS region. Is it ok to use CDS regions for DE analysis? if not, how can i predict the related exons from my assembled fasta file?

metatranscriptomics RNA-SEQ • 746 views

ADD COMMENT • link 2.9 years ago by shail.nair05 ▴ 20

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bacteria do not have exons. Therefore, it is ok using the CDS regions to generate count data

ADD REPLY • link 2.9 years ago by andres.firrincieli 3.6k

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Thank you. yes, i thought so.

ADD REPLY • link 2.9 years ago by shail.nair05 ▴ 20

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