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Old 02-08-2017, 12:31 PM   #1
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Default SE vs. PE for bacterial RNAseq

We plan an RNAseq analysis to study gene expression in a bacteria that we have an in house reference genome assembly (~7.8Mbp) and gene annotation (7000 genes) that we are very confident about (both).
in a previous RNAseq analysis we used 100bp SE reads with ~3M reads per sample (after QC) and got nice coverage and statistics for our gene expression study.

This time we will use a different service provider (due to some bureaucracy and budget issues) and they offered either ~7-8M reads of 80bp SE, or a similar number of reads but PE with 40bp length and around 350bp insert (for the same price).

Can anyone suggest me which offer to take ?
Thank you !
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Old 02-08-2017, 02:18 PM   #2
Brian Bushnell
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I would prefer 80bp SE to 40bp PE. I don't think it would have a significant effect on your results, but single-ended reads tend to be easier to work with.
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bacterial rna seq, gene expression, single end reads

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