[galaxy-user] Trimming small RNA

[Thiago Mafra]

Hello everybody,

I have sequences of small RNA's from 18 to 35nt and accurate trim the
sequences of the adapters before aligning the reads with the reference
genome. Are there any tools available to it in the Galaxy?

Thanks.

--
Thiago Mafra Batista
Biólogo Molecular
Doutorando em Bioinformática - UFMG
LGB - ICB/Bloco K4 sala 245
Tel Lab: (31) 3409-2628
CV: http://lattes.cnpq.br/9414909432933240
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Re: [galaxy-user] Trimming small RNA

[Richard Mark White]

Hi,
  This must seem like a newbie question but I cant get a clear answer.  My 
understanding from the galaxy wiki 
page http://wiki.g2.bx.psu.edu/Learn/FAQ#Learn.2BAC8-FAQ.Interval_and_BED_format
 is that all intervals in galaxy are 0 based, start inclusive end exclusive.  
but when i use generate pileup/filter pileup and convert to intervals, i get 
something like this:
 
chr10 1056309 1056310 G C +

When i look up the SNP (G--C) it is pretty clearly 1056310.  Which would make 
the interval end inclusive.  this is key because when i annotate snp's 
against dbSNP, i need to have the right cooridnates.

  Can anyone provide some guidance?  Thanks!

rich
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Re: [galaxy-user] Trimming small RNA

[James Robinson]

Hi Rich,

That is consistent with the BED format, that is in BEDs 0 based coordinate
system the SNP is at 1056309.   In the more common 1 based system this
translates to 1056310.  If the end were inclusive the SNP would be at
1056309-1056310 in BED world,  that is it would take 2 positions.

The first base of a genome in BED coordinates is represented as  0-1.

My quick rule of thumb for converting between coordinate systems is to add
(or subtract) 1 from the start base, leave the end base alone.

Jim

On Sun, Sep 11, 2011 at 10:58 PM, Richard Mark White whit...@yahoo.comwrote:

 Hi,
   This must seem like a newbie question but I cant get a clear answer.  My
 understanding from the galaxy wiki page
 http://wiki.g2.bx.psu.edu/Learn/FAQ#Learn.2BAC8-FAQ.Interval_and_BED_formatis 
 that all intervals in galaxy are 0 based, start inclusive end exclusive.
  but when i use generate pileup/filter pileup and convert to intervals, i
 get something like this:

 chr10 1056309 1056310 G C +

 When i look up the SNP (G--C) it is pretty clearly 1056310.  Which would
 make the interval end inclusive.  this is key because when i annotate
 snp's against dbSNP, i need to have the right cooridnates.

   Can anyone provide some guidance?  Thanks!

 rich


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 Galaxy analysis and other features on the public server
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 use the Galaxy Development list:

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 To manage your subscriptions to this and other Galaxy lists,
 please use the interface at:

  http://lists.bx.psu.edu/

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