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mtokuyama / ERVmap

ERVmap is one part curated database of human proviral ERV loci and one part a stringent algorithm to determine which ERVs are transcribed in their RNA seq data.
http://www.ervmap.com
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Differential analysis #10

Open ZunpengLiu opened 1 year ago

ZunpengLiu commented 1 year ago

Hi Maria,

Thank you very much for developing this robust tool!

I am conducting the differential ERVs analysis. I have a question regarding if we should take gene expression into consideration. Which way do you think is better? 1) calculate the differential ERVs based on the count of ERVs only. 2) calculate the differential ERVs based on the input file of the count of ERVs and genes (that basically means i will cat the two count files and conduct the differential ERV analysis with DEseq2)

Thank you so much!

Best,

Zunpeng

rkabiljo commented 1 year ago

Hello @ZunpengLiu , I don't know if this is still relevant. You can see the issue I opened today as it is related.
I am afraid that if I analyse ERVs separately, I will inadvertently double normalise as DEseq automatically estimates size factors. In order to overcome this, I have passed sizeFactor column set to all 1, so it will normalise but do nothing. Maybe the best option is what you suggested in point 2 - to not normalise using ERVMap perl script, to concatenate the two matrices and then to go to DEseq where estimateSizeFactors will be called. If you meanwhile have any more insight into this, please let me know.

JianGuoZhou3 commented 5 months ago

@ZunpengLiu Hi Zunpeng, I also have some issues with ERVmap, if you have free time please help me to check this issue. My email is jianguo.zhou@fau.de. Best, Jian-Guo https://github.com/mtokuyama/ERVmap/issues/7