Thank Chris.
I was a bit worried that I was doing something wrong.
On Thu, Aug 27, 2015 at 11:07 PM, Chris Hoefler <hoeflerb@xxxxxxxxx> wrote:
Depending on how you do your downstream analysis, there are several ways
to get just the mapped reads back. One is to use the
<assembly>_out_2015_seq.<un>padded.fasta file, which will not contain your
reference because you specified it as a different strain. Another is to use
miraconvert to output a SAM file without the backbone.
On Thu, Aug 27, 2015 at 9:26 AM, Chitra P <pattabiraman.chitra@xxxxxxxxx>
wrote:
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
--
Chris Hoefler, PhD
Postdoctoral Research Associate
Straight Lab
Texas A&M University
2128 TAMU
College Station, TX 77843-2128
