[mira_talk] Re: Request for help: demystifying Illumina paired-end format identifiers ... /4 ???
- From: Shaun Tyler <Shaun.Tyler@xxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 5 Oct 2013 19:21:47 -0500
Me again.
I just took a look at the paper and I think the issue might be due to the
data processing. They mention that they used CASAVA to extract the fastq
files. We've been running MiSeqs for a couple of years and we have never
used CASAVA. That was only used on our old GAIIx. As far as I know your
typical MiSeq data goes directly through RTA to generate the fastq files
and does not employ CASAVA.
It could be that the read assignment you are seeing is because this is old
data processed with legacy software or approaches. CASAVA could very well
assign read names differently than what we see now.
Just another guess.
Shaun
From: Shaun Tyler <Shaun.Tyler@xxxxxxxxxxxxxxx>
To: mira_talk@xxxxxxxxxxxxx
Date: 2013-10-05 06:30 PM
Subject: [mira_talk] Re: Request for help: demystifying Illumina
paired-end format identifiers ... /4 ???
Sent by: mira_talk-bounce@xxxxxxxxxxxxx
That would have also been my first guess but it doesn't jive. We run tons
of dual index Nextera libraries and the reads always have the 1 and 2
format. (BTW - the 3 read thing could be a hold over from TruSeq which
only allows for single indexing????). So here's another guess.
I haven't looked at the paper but is there a chance they used custom
indexes or sequencing primers. We've never done that but I know it can be
done. Perhaps in those situations Illumina opted to name things
differently in order to distinguish it from "normal" data. I see no reason
why they would do that and I've never seen anything in tech bulletins, etc
about this but you never know. Regardless this is bad form on their part.
Changes to data format is always a pain (like when they dropped the / )
but keeping it a secret ..................................
My suggestion is to simply call Illumina tech support and ask them. We run
a number of NGS platforms and when it comes to technical issues,
bioinformatics or otherwise, Illumina is by far the most responsive. And
I've never spent more than a minute or so listening to bad elevator music
before talking to a warm body ;-)
Shaun
Inactive hide details for "Langhorst, Brad" ---2013-10-05 06:46:00 AM--->>
<read number> will typically be 1 or 2, but the fie"Langhorst, Brad"
---2013-10-05 06:46:00 AM--->> <read number> will typically be 1 or 2, but
the field can support other values. (For example, ce
From: "Langhorst, Brad" <Langhorst@xxxxxxx>
To: "<mira_talk@xxxxxxxxxxxxx>" <mira_talk@xxxxxxxxxxxxx>
Date: 2013-10-05 06:46 AM
Subject: [mira_talk] Re: Request for help: demystifying Illumina paired-end
format identifiers ... /4 ???
Sent by: mira_talk-bounce@xxxxxxxxxxxxx
>> <read number> will typically be 1 or 2, but the field can support other
values. (For example, certain indexing formats lead to 3 reads.)
>>
>> Fine, so Illumina says there can be up to 3 reads (but are not saying
how they name that). So why am I seeing a value of 4?
Hi… just a guess
2 insert reads
2 index reads
R1 = insert 1
R2 and R3 index reads
R4 = insert from other direction
I don't think it's bad faith for illumina to extend and add more reads …
but shifting the meaning of the names is really quite lame.
Brad
--
Brad Langhorst
Applications and Product Development Scientist
--
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