what are the advantages of single-end sequencing?

[szy0931]

since we can use double-end sequencing, why do you do and at what situation will you do single-end sequenicng?

[vivianshaw]

Probably is the simplest way to utilize Illumina sequencing. And Single-read sequencing can be a good choice for certain methods such as small RNA-Seq or chromatin immunoprecipitation sequencing (ChIP-Seq).

[Ben3]

szy0931 single-end reads are cheaper and faster, especially if the sequences you're looking for are already known. For example, we used single-end reads a lot for pathogen detection because we knew which pathogens might be in the sample, and if they were present, we could get enough coverage for the single-end reads.

[szy0931]

szy0931 single-end reads are cheaper and faster, especially if the sequences you're looking for are already known. For example, we used single-end reads a lot for pathogen detection because we knew which pathogens might be in the sample, and if they were present, we could get enough coverage for the single-end reads.

You said cheaper. Do you mean save an index? I understand faster.

[Ben3]

szy0931 no, I mean cheaper because with pair-end runs you have to buy a kit with twice as many cycles. For example, we normally ran a 75-cycle kit and if we wanted pair-end sequencing we would have needed a 150-cycle kit. So the lower cycle kits are usually about half the price. This saved us a lot of money and we could sequence many more samples.