Number of transcripts in report

[karini925]

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]

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

[rkabiljo]

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.