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mlbendall / telescope

Quantification of transposable element expression using RNA-seq
MIT License
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Number of transcripts in report #10

Open karini925 opened 4 years ago

karini925 commented 4 years ago

I have successfully run Telescope on ~500 samples with a report produced for each sample. These have varying levels of ERVs reported in the report. Some ERVs have final counts of 0s and I am assuming ERVs that are not present in the report could not be aligned. How would you recommend to conduct a differential expression analysis across these 500 samples with varying numbers of ERVs reported - would it be fair to label the missing ones as 0 final counts and do it that way? thanks!

vinegang commented 2 years ago

I have the same concern. how did you proceed with your analysis?

rkabiljo commented 2 years ago

I am also following this as I noticed the same issue. Many transcripts are with counts 0, and many are missing from the report, and I am also thinking of whether it is safe to set them all to 0.