Hi everyone,

I am using the [EstimateLibraryComplexity][1] utility from Picard Tools to calculate the complexity of my paired-end RNAseq libraries.

 [1]: http://picard.sourceforge.net/command-line-overview.shtml#EstimateLibraryComplexity

This is my command line:

    java -jar /picard/EstimateLibraryComplexity INPUT=sample.bam OUTPUT=sample_libcomp.txt VERBOSITY=ERROR VALIDATION_STRINGENCY=SILENT

This generates a `sample_libcomp.txt` file. This is the truncated output:

```
## HISTOGRAM    java.lang.Integer
duplication_group_count    P01311

1       23739815
2       3633946
3       870509
4       426481
5       202751
6       171461
7       93221
8       83632
9       58171
10      50066
11      34938
12      36788
13      24277
14      24100
15      19388
16      18345
17      13640
18      14480
...
456     1
457     1
458     1
459     1
460     2
464     3
468     1
470     2
471     2
473     1
477     2
480     1
484     1
488     1
```

Can anyone explain to me what these values mean? I couldn't find an explanation of the output anywhere. I plan to plot these values as a density histogram (maybe convert the values to log2). So I really need to understand what these values are in order to interpret the histogram that I will create later.

Thanks!
<p>The first column is the number of duplicates. The second column is the number of reads having the corresponding number of duplicates.</p>

<p>So in your output, there are 426,481 sequences which have exactly four duplicates.</p>
