differences in number of reads between *frag.gz and frag_raw.gz files

[Former user]

Hi,

I've noticed a discrepancy on the number of reads included the output to the *frag.gz and frag_raw.gz files. Is there any reason for this?

Lorcan

[ptlcc]

Hi Lorcan

The frag_raw file contains the mappings (or alignments depending on the options) from query sequences against all templates in your index.
The frag file contains the query sequences which aligns to an overrepresented template.
This means that the frag_raw file might contain more reads than the frag file.

Best,
Philip

[alvanuffelen]

Hi

What are the criteria for a template to be overrepresented?