On 01/20/11 09:06, Stephen Taylor wrote:
Hi Peter,
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).
... oops, -osformat for sequences of course.
Sadly, fuzznuc doesn't seem to work using aformat or oformat. Is that
due to be supported?
Ah, fuzznuc reports features so we hadn't implemented SAM there.
However, you can use -rformat listfile to get USAs for the features, and
then seqret -osformat sam @listfilename to get the sequences in SAM format.
Possibly scope to do more there. What would you like to see in SAM
output for fuzznuc?
regards,
Peter
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