[mira_talk] Re: Mira results much worse than newbler
- From: Robin Kramer <kodream@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 16 Jul 2011 07:16:10 -0600
Well sffinfo worked.
I am guessing it is a newer version or something.
On Sat, Jul 16, 2011 at 1:26 AM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> > Betreff: [mira_talk] Re: Mira results much worse than newbler
> > Maybe this is the only one but I had a bear of a time getting this
> > one to work, and I expected that it wasn't a bug but just how sff_extract
> worked.
> > The SRA sample SRR054580 demonstrates it though.
>
> A specific SRA ... now we're getting somewhere.
>
> > Since it was in the SRA I couldn't contact the sequence provider,
> evidently
> > using minleft clip does exactly that. However going back and trying it
> on
> > other sequences it does indeed seem to do exactly the same as sffinfo
> when it works.
>
> It's not "when" sff_extract works ... when extracting non-paired sequences
> it *always* works like sffinfo.
>
> >
> ********************************************************************************
> > WARNING: weird sequences in file SRR054580.sff
> > After applying left clips, 513937 sequences (=57%) start with these
> bases:
> > A
> >
> > This does not look sane.
> > ...
>
> This warning message is courtesy of sff_extract: the SFF is very probably
> broken. sff_extract caught that and gave you a warning, which, by the way,
> you do not get in sffinfo. The resulting FASTA file both from sffinfo and
> sff_extract are still exactly the same.
>
> B.
>
>
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