[mira_talk] Re: info files
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 21 Apr 2009 22:42:36 +0200
On Tuesday 21 April 2009 Shai Uliel wrote:
> 1)
> One cluster From my clusters:
> >lcl|reads_lrc19975 No definition line found
>
> From file info/reads_info_consensustaglist.txt
>
> reads_lrc19975 10 10 10 10 IUPc Strain'default': S
> reads_lrc19975 12 12 12 12 IUPc Strain 'default': Y
>
> 12345678901234567890
> TGTACAATCGSCYGGGGGAG
> It look like the location need to be 11 and 13. And not 10 12 (1 bp
> shift)
Hello Shai,
ah, the index of a lot of files written by MIRA start at 0, not at one. A
permanent cause of confusion when it comes to programmers/users :-)
012345678901234567890
TGTACAATCGSCYGGGGGAG
Now it fits :-)
> 2)
> [...]
> The number from reaTo from file reads_info_readtaglist.txt are more
> than the length of seq!!!!
I'd need to check, but I think to recall right if I say that these positions
are for "padded" read positions.
E.g.:
Read 1: AAAAAAC
Read 2: AAATTTAAAC
Alignment:
Read 1: AAA***AAAC
Read 2: AAATTTAAAC
Assuming that the "C" at the end of both reads get tagged, it'd get a position
larger than the read is long before the alignment.
Then again, I suppose I should also add an "unpadded, original" position to
that output file. Is easily doable, I've put it on the TODO.
Thanks for your feedback :-)
Regards,
Bastien
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