jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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discrepancy in reports between cutadapt and atropos on the "expect" column #42

Closed cokelaer closed 6 years ago

cokelaer commented 6 years ago

Here is a sample of a cutadapt report for a given adapter:

Overview of removed sequences (5')
length  count   expect  max.err error counts
6   7   24.4    0   7
7   3   6.1 0   3
10  1   0.1 1   0 1
11  1   0.0 1   0 1
12  1   0.0 1   1

and atropos 1.1.14 reports:

Overview of removed sequences (5'):
length count expect max.err error counts    
                                    0 1         
------ ----- ------ ------- ------------
     6     7  146.3       0   7           
     7     3   36.6       0   3           
    10     1    4.6       1   0 1         
    11     1    2.3       1   0 1         
    12     1    1.1       1   1           

Everything is identical but the third column (expect) that is 6 times the values reported in cutadapt. Not sure what is the reason for this difference, and whether is a bug or intended behaviour.

jdidion commented 6 years ago

I think I've figured this out, but I'd like to test it on some real-world data to make sure. Can you provide a sample fastq and the atropos command you used? A subset of ~10000 reads should be enough. Thanks