[mira_talk] Re: More than two reads for one <template_id>
- From: Nestor Zaburannyi <nestor@xxxxxxxxxxxxx>
- To: Bastien Chevreux <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 20 Jul 2011 21:12:48 +0200
Dear Bastien,
> On Wednesday 20 July 2011 14:32:25 Nestor Zaburannyi wrote:
>> For one dataset (454 PE) i got such messages:
>> "The reads X, Y, Z, W have the same template and MIRA was unable to
>> differentiate between different trials. Template information not used
>> there."
> Strange ... did the data come straight out of sff_extract or does it contain
> something else? Because that would mean there's a bug in the PE extraction
> module there then :-(
> Or you have identical reads in different SFFs (possibly through repackaging).
> Or reads in different SFFs are named identically, but I though that 454
> changed their naming already quite some time ago to make that almost
> impossible.
Hmm... To tell you the truth, i really don't know how files were generated. I
can even show you "THE file":
ftp://ftp.ncbi.nih.gov/pub/TraceDB/streptomyces_albus_j1074/fasta.streptomyces_albus_j1074.001.gz
If you are interested, you can view it and search for ".T1" and four
surrounding reads. Those will be
>gnl|ti|2099518166 BI018061e870732a2cbb74c44d34e95a17.F.6.T0
>gnl|ti|2099518167 BI018061e870732a2cbb74c44d34e95a17.F.6.T1
>gnl|ti|2099518168 BI018061e870732a2cbb74c44d34e95a17.R.6.T0
>gnl|ti|2099518169 BI018061e870732a2cbb74c44d34e95a17.R.6.T1
all the four reads have correspondingly
<TRACE_ID>BI018061e870732a2cbb74c44d34e95a17</TRACE_ID>
in *.xml file.
You'll then see what i mean.
> Could yopu please check which of the above may be what's hitting you?
>> Really, there are several reads (up to 6) for one template_id, but this
>> happens rarely (approx. 1000 of such templates). Should i just ignore this
>> message, or should i split them to unique pairs by using the TRACE_NAME
>> field which is different for every F/R pair?
> If there are only a few, you can as well let MIRA continue.
> B.
Sincerely yours
Nestor
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