Question: where does the count.txt file come from?

[mad-scientist-in-training]

Hi,

I'm trying to run the chaining script, and I'm curious where the count.txt file come from:

SAMPLE=;
SAMPLE=;

GROUP_FILENAME=touse.group.txt
GFF_FILENAME=touse.gff
COUNT_FILENAME=touse.count.txt
FASTQ_FILENAME=optional.rep.fastq

I ran the collapse script and so I have the group.txt and the gff files - is the count.txt file the same as the abundance file produced from get_abundance_post_collapse.py script? If it is, does it need any modification?

Thanks so much!

Camille