[mira_talk] Re: New Solexa seqence identifier format - Paired end reads

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Mon, 16 Apr 2012 01:55:40 +0200

On Apr 16, 2012, at 1:35 , Alexis Blanchet-Cohen wrote:
> I will concatenate the two paired end read files, with the old format 
> sequence identifier line, and run MIRA overnight.
> I'm assuming that no shuffling is required as for the Velvet assembler, and 
> one can simply paste the second file at the end of the first file.

Correct.

>> Try
>     sed 's/^@\(.+\) \(.\)/@\1\/\2 \2/' infile >outfile
> 
> It didn't seem to work. Perhaps a mistake on my part.

Nope, my bad. This is a working one:

  sed 's/^@\(.*\) \(.\)/@\1\/\2 \2/'

and for the people fearing changes in the future, one could use:

  sed 's/^@\([^ ]*\) \([^:]*\)/@\1\/\2 \2/'

B.



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