Does breadth of coverage signify expression?
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3 months ago
Smriti ▴ 20

Hi all!

Against my reference human transcriptome, for all 112 dengue samples (categorized into mild, moderate and severe), I see breadth of coverage (%) ranging from 0.002 % to 0.09 %. and transcript count is ranging from 1 % to 26 %. Now since this is the range when only unique or longest transcripts were considered (that means excluding redundance exons or transcript isoforms), my transcript count is equivalent to expressed gene count.

But i am still unable to make the understanding of how my coverage breadth and expressed count differs or how it is similar or relative? What does it really signify that my one sample that has a coverage of 0.043% has transcript count of 15.77%? ....Does this mean that of my whole transcriptome, only 0.043% could be covered (horizontally) by my sequencing reads present in one sample and this proportion of 0.043 account for 15.77% of all transcripts that are there in whole transcriptome (but considering only unique ones from all)???

P.S: I used bedtools to get coverage and only focused on at a depth of 5 to 10.

Thanks

Coverage breadth Bedtools Expression count • 173 views
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