Changes between Version 28 and Version 29 of SOPs/InProgress

Timestamp:

12/02/15 15:30:19 (9 years ago)

Author:

ibarrasa

Comment:

--

SOPs/InProgress

@@ -1 @@
-These are some useful references:
+'''Calculating number of reads needed for certain coverage'''
+
+* 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 for 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/]
 
 
-Ref1 for estimates of the number of reads required for single
-nucleotide variant calling: [http://www.ncbi.nlm.nih.gov/pubmed/21771779/]
+ *  ''Example 1''
 
-Ref2 for estimates of the number of reads required for single
-nucleotide variant calling: [http://www.ncbi.nlm.nih.gov/pubmed/24434847]
+ For a  3e+9 nt genome if we want 35x coverage we would need: 
 
-For estimates of the number of reads required for RNA-seq
-and ChIP-seq experiments: [http://www.ncbi.nlm.nih.gov/pubmed/24434847/]
+ 3e+9 * 35 / 40 = 2.625e+09 = 2.6 billion 40-nt reads[[BR]]
+ or[[BR]]
+ 3e+9 * 35 / 100 = 1.05e+09 = 1 billion 100-nt reads
 
-Example 1
 
-For a  3e+9 nt genome if we want 35x coverage we would need: 
+ *  '' Example 2''
 
-3e+9 * 35 / 40 = 2.625e+09 = 2.6 billion 40-nt reads[[BR]]
-or[[BR]]
-3e+9 * 35 / 100 = 1.05e+09 = 1 billion 100-nt reads
+ For an RNA_seq experiment:
+ If we have 6 million paired end reads and a genome with ~7000 genes expressed X 5741 bp 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.[[BR]]
+ 420 mill nt that we will cover/ 40 mill nt to cover ~ 10 x coverage.
 
 
 
-Example 2
-
-For an RNA_seq experiment:
-If we have 6 million paired end reads and a genome with ~7000 genes expressed X 5741 bp 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.[[BR]]
-420 mill nt that we will cover/ 40 mill nt to cover ~ 10 x coverage.
-
-
-