Intermediates and Filtering

After the initial group calling the BRASS flow progressively filters the groups down via several methods.

Some of the intermediate files are available in *.intermediates.tar.gz ordered as follows:

1. .groups.gz - raw brass group output
2. .groups.filtered.bedpe
3. .groups.clean.bedpe

groups.gz

This is the raw output from the grouping algorithm:

• cols 1-4 LOW chr, strand, start, stop
• cols 5-8 HIGH chr, strand, start, stop
• N columns of read counts from each sample (see #NSAMPLES in header) ordered as per the header
• Hits repeat (. unless repeat filtering was used)
• N columns of read NAMES from each sample (see #NSAMPLES in header) ordered as per the header