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I have 2 sets of fastq files from another collaborator. The first is contains exome data and the second contains RNAseq data. But both have the RNA in the name but a different ID. How do I differentiate between a fastq file between exome seq and RNAseq?

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welcome to the Bioinformatics StackExchange! This is one of those cases where the best solution is to just ask your collaborators. Don't bother with anything technical from the data itself because it's only going to waste your time.

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Absolutely agree with James that you should ask your collaborators, but purely as an academic exercise... assuming you have a good reference genome+annotation (e.g. human/mouse), whole exome seq should align to mostly annotated exonic, RNA-seq to exonic+intronic, and whole genome seq to exonic+intronic+intergenic sequences. Sequence duplication levels may also be higher for RNA-Seq with highly expressed genes often 'deeply' sequenced

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  • $\begingroup$ Adding on this, in WES one sonicates DNA and then captures it. Due to random sonication the coverage around exons should (on the genome browser) look gaussian/bell-shaped. In RNA-seq the transcription start is a precisely defined position, so the coverage at the TSS should bimodally ramp up, same goes for coverage at splice sites, aka it should not be bell-shaped. $\endgroup$
    – ATpoint
    Apr 4, 2023 at 15:34

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