normalization across different species for DESeq2 analysis
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piemmea • 0
@c2113756
Last seen 7 days ago
Italy

Hi, I am willing to try to perform a kind of differential analysis using DESeq2 among two groups of different species (same genus).

I read what was posted previously in this link but unfortunately I cannot reply that workflow since there is only one genome available so that I have to map everything against it. Problem is the systematic bias I create, given (also) that the two groups have different mapping rates, with one with higher similarity to the sequenced genome than the other group.

I am aware that such approach is quite 'unadviceable' but still if anyone believes there is a way to do it, it would be very appreciated ^_^

Since I assembled the RNAseq reads using Trinity, maybe I could use with that the approach used in the post above with some modifications: given the redundancy in Trinity maybe I could use the Supertranscripts and recognize the supposed orthologs based on Blast reciprocal best hit? I do not think that just lowering the mapping stringency would help.

Many thanks for your advices!

DESeq2 normalization Normalization acrossspecies • 127 views
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@mikelove
Last seen 3 days ago
United States

There are many posts on this topic, in addition to that one:

https://www.google.com/search?q=site%3Asupport.bioconductor.org+DESeq2+across+species

I don't have any advice on how to interpret DE when it is confounded with high vs low mapping rate, due to use of a reference genome of one of the two groups.

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