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Old 10-16-2012, 07:14 PM   #1
gary
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Location: Shanghai

Join Date: Dec 2009
Posts: 16
Default MarkDuplicates result

Hello everyone!

My MarkDuplicates result looks like this:
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
TSC_3 351087 23255402 695866 192406 1108098 370488 0.051398 347340970

## HISTOGRAM java.lang.Double
BIN VALUE
1.0 1.015653
2.0 1.965532
3.0 2.853897
4.0 3.68473
5.0 4.461759
6.0 5.188466
7.0 5.868112
8.0 6.503743
9.0 7.098211


My question is:
what does the ESTIMATED_LIBRARY_SIZE mean?
Picard's help info is: ESTIMATED_LIBRARY_SIZE: The estimated number of unique molecules in the library based on PE duplication.
But I still can't understand.

Last edited by gary; 10-16-2012 at 07:17 PM.
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Old 03-27-2013, 07:07 AM   #2
davidblaney
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Default

The Estimated number of unique fragments in your sequenced library.

it uses this (from the API documentation)

Quote:

Estimates the size of a library based on the number of paired end molecules observed and the number of unique pairs ovserved. Based on the Lander-Waterman equation that states: C/X = 1 - exp( -N/X ) where X = number of distinct molecules in library N = number of read pairs C = number of distinct fragments observed in read pairs

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