Question: Transcriptome Coverage- Method Of Calculation
2
gravatar for nayaganviji
6.5 years ago by
nayaganviji20
nayaganviji20 wrote:

how we calculated transcriptome coverage of non model species like Crow. i am plan to use GS FLX+ system for RNA sequencing.

seq rna • 3.5k views
ADD COMMENTlink written 6.5 years ago by nayaganviji20
2
gravatar for JC
6.5 years ago by
JC7.7k
Mexico
JC7.7k wrote:

It's really complex, because transcripts are not distributed proportionally. Many genes will be expressed in 10-100's copies but very few will be in the order of 1000's and others in <10's, so a minimal coverage should include low expressed genes but you will have to reduce the highly expressed genes to maximize your chance to get them in the sequencing. Besides, the non-model specie makes this harder to estimate. Additionally, the sample is also a factor, in humans, the brain express a more diversity range of transcripts than other tissues.

*I almost mark this question as duplicate of your last one, but the question is more specific. Maybe you can try to combine your questions because they are related.

ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by JC7.7k
1
gravatar for Ketil
6.5 years ago by
Ketil3.9k
Germany
Ketil3.9k wrote:

To calculate average coverage, you take the total amount of sequence, and divide by the total size of the transcriptome. If you don't know the latter, you can get an estimate by clustering the reads, but this will have huge opportunities for error.

Minimum coverage is likely zero (many transcripts will not be expressed), and maximum coverage is typically some ribosomal RNAs, which can be 30-50% of your reads.

ADD COMMENTlink written 6.5 years ago by Ketil3.9k
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