Changes between Version 26 and Version 27 of SOPs/InProgress

Timestamp:

12/02/15 13:37:08 (9 years ago)

Author:

ibarrasa

Comment:

--

SOPs/InProgress

@@ -1 @@
-None at this time
+These are some useful references:
+
+
+Ref1 for estimates of the number of reads required for single
+nucleotide variant calling: [http://www.ncbi.nlm.nih.gov/pubmed/21771779/]
+
+Ref2 fFor estimates of the number of reads required for single
+nucleotide variant calling: [http://www.ncbi.nlm.nih.gov/pubmed/24434847]
+
+For estimates of the number of reads required for RNA-seq
+and ChIP-seq experiments: [http://www.ncbi.nlm.nih.gov/pubmed/24434847/]
+
+Example 1
+
+For a  3e+9 nt genome if we want 35x coverage we would need: 
+
+3e+9 * 35 / 40 = 2.625e+09 = 2.6 billion 40-nt reads
+or
+3e+9 * 35 / 100 = 1.05e+09 = 1 billion 100-nt reads
+
+
+
+Example 2
+
+For an RNA_seq experiment:
+If we have 6 million paired end reads and a genome with ~7000 genes expressed X 5741 pb average gene length = 40,187,000. That is 40 mill nt to cover.
+
+6M reads x 70 bp (35 pb per paired end reads) = 420 mill bp that we will cover.
+420 mill nt that we will cover/ 40 mill nt to cover ~ 10 x coverage.
+
+
+