Hi all,
I am really new to MIRA and assembly. I am mapping some IonTorrent reads
to a reference genome ( the genome has multiple segments, each segment has
unique NCBI identifier).
Here is the problem: In my project_info_contigreadlist.txt, the reference
segment of the genome is listed as a read.
I am worried about this as it might inflate the actual coverage and suggest
that I have information on regions that my sequencing results actually do
not cover.
Why does this happen?
This is how my manifest file looks.
project = project_2
job = mapping,est,accurate
parameters = IONTOR_SETTINGS
readgroup
is_reference
data = /ref/ref.fna
strain_name = 2015_ref
readgroup = S9
data = /IonProton07082015/S9.fastq
technology = iontor
strain_name = 2015_seq
I would really appreciate some help with understanding this.
Many thanks,
Chitra