Thanks for your email.
I am very confused with the result.
Below is a part of the .tcs file converted from the mira output .caf file using
CAF_2_TCS.py
[…]
Ummmm, CAF_2_TCS.py is nothing I wrote. Who’s the author, have you tried to
contact him?
What does MIRA tell you in its result files (FASTA) what the seemingly wrong bases
are? Are these correct? If yes, this would really be a strong indicator >for a
bug in the py script and not in MIRA.
The result fasta file in the mira results folder for these bases are not
correct either. They are the same as it in the TCS.
I wrote my own R program to parse the .caf file from mira's output, and got the
same information as CAF_2_TCS.py.
I also tried to convert the fastq to fasta file and set the default_qual = 50
and use the fasta file to do the same mira assembly,
and I got the perfect results.
I mean the .fasta in the mira output folder looks perfect, so as the TCS file
and my own results.
Since we know what our sample is, it should be very similar to the reference
(maybe with a couple of mutations in every 1kb).
When we use the fastq to do the assembly, the result shows lots of mutations.
And when I checked the .caf file use CAF_2_TCS.py
or my own R program, and I found that many of the "Mutations" actually are not
mutations, for example, for a base, there are
more than 20k "A", and only less than 100 "C","T","G" and "*", I expected the result for
this base to be "A", however, the result file shows
a "G" for this base. And we had quite a lot this kind of cases.
However, if I use the fasta file to run mira, we do not have this kind of
problems at all.
So I am wonder whether there is some problem with our .fastq file or something
else.
Thank you very much for your help.
Best wishes,
Yongmei
________________________________________
From: mira_talk-bounce@xxxxxxxxxxxxx [mira_talk-bounce@xxxxxxxxxxxxx] On Behalf
Of Bastien Chevreux [bach@xxxxxxxxxxxx]
Sent: Thursday, January 23, 2014 3:31 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: Questions on consensus sequence vs .TCS file
On 23 Jan 2014, at 3:41 , yongmei <yongmei@xxxxxx> wrote:
I am very confused with the result.
Below is a part of the .tcs file converted from the mira output .caf file using
CAF_2_TCS.py
[…]
Ummmm, CAF_2_TCS.py is nothing I wrote. Who’s the author, have you tried to
contact him?
What does MIRA tell you in its result files (FASTA) what the seemingly wrong
bases are? Are these correct? If yes, this would really be a strong indicator
for a bug in the py script and not in MIRA.
I also tried to convert the fastq to fasta file and set the default_qual = 50
and use the fasta file to do the same mira assembly,
and I got the perfect results.
I’m not sure if I understood your last sentence correctly. What result is
perfect? The TCS?
B.
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