quick question on paired RNAseq reads

Question

[leohawk]

a quick and naive questions, handling a paired read RNAseq dataset on human genome. left mapped and right mapped are both around 20 million(tophat2), so for the coverage, shall we say it is 20 million or, since it was sequenced from both end, shall we say the total read is 20 * 2, 40 million?

By the way, is around 30 to 30 million mapped is good enough for a typical human RNAseq experiment?

Answer 1

[Kamil]

If you have 20 million pairs of reads, then you have 40 million total reads. Since RNA-seq is commonly paired-end nowadays, people often refer to fragments rather than reads. For each fragment (DNA molecule), you sequenced some of the bases at the start of the fragment and some of the bases at the end of the fragment.

For a general introduction to all aspects of RNA-seq, check out:

• RNA-seqlopedia

30 million mapped fragments is enough to do differential expression analysis. It might even be enough to do splicing analysis and variant calling.

Please see this post for more discussion:

• How Much Coverage Do We Need For An Rna-Seq Experiment?

[leohawk]

Thanks for your input, many thanks...