[mira_talk] less number of reads used
- From: Manoharan <manoharan.k@xxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 10 Apr 2014 10:20:41 +0530
Dear All,
I am trying to run mira for ion proton plant transcriptome data(2 GB)
mean read length is between (90-130) for all the 6 sample together. It
comes under solanum genus. In the assembly only 20% reads are used.
Is it likly possible because low data or I am lacking in parameters?
Please find below parameter which I have used. For Ion data is it trim
the low quality bases (phred<20) By default it trims (phred<15) I have
used default?
project = sample1
job = est, denovo, accurate
parameters = COMMON_SETTINGS -GE:not=30 \
--noclipping \
IONTOR_SETTINGS -AS:mrpc=50
readgroup = ion_single
technology = iontor
data = sample1.fastq
I have another question regarding Whole genome denovo assembly for
bacteria. It is a 5 MB Genome. I have obtained 80X coverage (Ion proton)
data (mean read length 150). But after assembly (I am getting >2000
contigs). For this also I have used same above parameter except est
option. I have two doubts,
What could be the reason for more number of contigs(may be repeat, GC,
Genome complexity) but how to find out which is the one?
or Is there any problem in the parameter?
Looking forward for your help,
Regards,
Manoharan
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