[mira_talk] Re: not=4 does not appear to be working on my Mac OS; system freezes after long read name lengths
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 2 Sep 2014 21:21:30 +0200
On 02 Sep 2014, at 18:53 , Chris Hoefler <hoeflerb@xxxxxxxxx> wrote:
> […]
I’ve been playing catch-up with this thread this evening and it made me cringe
a couple of times.
First, thanks Chris & Rick for your answers, I couldn’t have formulated a
couple of things in your help better than you did.
John … you are in a position you should have never come to in the first place:
having sequencing data (part of it maybe unusable for what you hope to do) and
no idea what to do with it. This is not a reproach I make to you, but rather to
whomever sold you the sequencing service without ensuring that it would be
usable to you and your colleagues. Unfortunately I see this scenario every once
in a while and it makes me a bit sad.
However, one thing that you should be clear about is the following question:
“what do I want?” Metaphorically speaking, that is. WRT your problem, that
would be: “what are the questions we hope to answer from the sequencing data”
This is *the* single most important aspect which you need to be able to respond
to when going into a sequencing project as this determines what sequencing
technology and the sequencing depth you will need to get what you need.
And yes, even the “we want to have a first look at the genome and make
preliminary analyses” answer needs to be elucidated a bit more like: what kind
of analyses? SNPs? absence/presence of single genes? comparison to other
genomes? etc.pp
All the above should have been discussed with the sequencing provider first as
they would have probably given help in what is possible (and what not) with
given technologies and coverages.
Now, I really recommend that you seek sequencing AND bioinformatics support
(sequencing alone is not sufficient, you need to analyse the data!) with a
university core sequencing group or commercial provider to see what you can do
with what you have and, if needed, what it would need to get you what you want
or need. Most will be happy to talk to you if they sense there’s also something
in there for them.
Hope this helps,
Bastien
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