Using -D option

[Tejaswi Yarra]

Hello,

I have a question about removing duplicates from the sequences using the -D option.
I am unsure as to what the number N represents.

The documentation indicates:
-D N Remove duplicate reads : Read_1 has an identical N bases (0)

If I do "-D 50" then Read_1 has 50 identical bases? What does this actually mean?
How can I actually use this option to remove duplicate sequences from my data?

Thank you in advance for your help and apoligies if my question was very amateurish.

Regards,
Teja.

[Jason Powers]

Teja,

The N here refers to the number of bases examined for duplication.

Let's say your read is a single-end fastq that is 50 nt long.

If you set N to 25, then it is going to find all unique 25mers (starting from the first base), and toss any duplicates.

[Tejaswi Yarra]

Thank you very much for the explanation Jason!
Very sorry for the late reply, I did not check back here in a long time.