reads and coverage question

[seqgirl123]

I am new at this and trying to wrap my head around understanding some terminology and how it all fits into the sequencing analysis side. So here are 2 questions:

1. When someone says they desire to have a lot of reads in their Illumina sequencing, is this the same as saying they are asking for a high coverage? For example, someone says they want a lot of reads for their library, so would this be like saying they are asking for 100x coverage where coverage is the way of quantitating (100x) how many reads they desire?

2. Are coverage and sequencing read depth the same thing?

[SeqAA]

Some applications need more reads than coverage. They are usually related but it can be more important to get one over the other in some cases.

In expression and counting applications you want read #'s more than read length and coverage.

In Chip Seq I would rather have 30 million 36bp reads rather than 15million 72bp reads. Same coverage, but one has more reads.

[tonybolger]

1. When someone says they desire to have a lot of reads in their Illumina sequencing, is this the same as saying they are asking for a high coverage? For example, someone says they want a lot of reads for their library, so would this be like saying they are asking for 100x coverage where coverage is the way of quantitating (100x) how many reads they desire?

You can increase coverage by having more reads or longer reads, so they're not quite the same thing. When working with a reference, reads which are 'long enough to be unique' are optimal, so you're better off spending your additional bases on more reads. For denovo, 'longer' is generally more important than 'more'.