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Different mappings, different PCAs using TEtranscripts
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16 months ago

Hello,

I made two PCA plots from two types of mappings towards the same genome. In one of them, I allow the reads to just map to one loci, and in the other one I let them map 100 times. After that I do transcript assembly with StringTie in the uniquely mapped reads, and i use the software TEtranscripts for the multi mapped reads (this plot is made just with the gene read counts).

The PCA plots look pretty different: The "unique" mapping separates the two conditions pretty well, and the other one not (not at all). I was wondering if I can still trust the results from the second mapping, or what does this really mean?

Thanks!!

Uniquely mapped:

pca-copy

Multi mapped:

pca-copy

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Based on which features is the PCA plot, and on how many of them, or on all genes?

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The unique mapping is made with transcripts (79,000), TEtranscripts outputs gene read counts so it is less (24,333 genes).

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TETranscripts is a very odd choice for this situation and I'm not sure how well it will perform given that it's meant to be used with genomic alignments in the context of a well-annotated genome (with repeats). Please use something like salmon instead.

What organism is this?

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Thank you for your answer. This is human data, and I am using the repeat information that TEtranscripts offer for other analysis.

I was expecting similar results from the two approaches and was wondering if there was a reason behind it. Even if the software was not specifically designed to only work with gene counts, I think it is relevant to make sure the conditions are being somehow differentiated if the software will perform a DEA afterwards.. Don't you think?

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There's no need to perform transcript assembly with humans (don't bother with stringTie). What this suggests is that repeat expression is dominating things and not different by condition.

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Thank you for your answer!

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