[mira_talk] Mapping Reads: Reference appears in the contig read list

  • From: Chitra P <pattabiraman.chitra@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 27 Aug 2015 19:56:56 +0530

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

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