Changes between Version 27 and Version 28 of SOPs/InProgress


Ignore:
Timestamp:
12/02/15 13:45:56 (9 years ago)
Author:
thiruvil
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/InProgress

    v27 v28  
    55nucleotide variant calling: [http://www.ncbi.nlm.nih.gov/pubmed/21771779/]
    66
    7 Ref2 fFor estimates of the number of reads required for single
     7Ref2 for estimates of the number of reads required for single
    88nucleotide variant calling: [http://www.ncbi.nlm.nih.gov/pubmed/24434847]
    99
    … …  
    1515For a  3e+9 nt genome if we want 35x coverage we would need:
    1616
    17 3e+9 * 35 / 40 = 2.625e+09 = 2.6 billion 40-nt reads
    18 or
     173e+9 * 35 / 40 = 2.625e+09 = 2.6 billion 40-nt reads[[BR]]
     18or[[BR]]
    19193e+9 * 35 / 100 = 1.05e+09 = 1 billion 100-nt reads
    2020
    … …  
    2424
    2525For an RNA_seq experiment:
    26 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.
     26If 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.
    2727
    28 6M reads x 70 bp (35 pb per paired end reads) = 420 mill bp that we will cover.
     286M reads x 70 bp (35 pb per paired end reads) = 420 mill bp that we will cover.[[BR]]
    2929420 mill nt that we will cover/ 40 mill nt to cover ~ 10 x coverage.
    3030