[mira_talk] Re: info files

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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