[EMBOSS] SAM format

Stephen Taylor stephen.taylor at imm.ox.ac.uk
Thu Jan 20 09:17:45 UTC 2011

On 20/01/2011 08:16, Peter Rice wrote:
> On 01/19/11 16:09, Stephen Taylor wrote:
>> Hi,
>> Is EMBOSS planning to release tools that produce SAM format in the near
>> future or is it more likely to be on the customary July 15th release?
> The last release EMBOSS 6.3.1 has SAM as an output format for sequences
> and pairwise alignments (-oformat sam and -aformat sam respectively).
> What data would you like to represent in SAM format, and are there extra
> fields you would like us to include?


Is there a bug in the gff3 output of fuzznuc?

##gff-version 3
##sequence-region chr21 1 46944323
#!Date 2011-01-20
#!Type DNA
#!Source-version EMBOSS 6.3.1
chr21   fuzznuc nucleotide_motif        13362906        13362942        37.000  +       .       ID="chr21.1";note="*pat pattern"

It would be nice to actually show the pattern matched in the note field.



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