[EMBOSS] run parameters for inexact matching with EMBOSS needle

David Mathog mathog at caltech.edu
Mon Feb 4 18:32:20 UTC 2019

On 04-Feb-2019 09:57, David Mathog wrote:
> lastal -P $CPUS -T1 -I80 -Y80 -m250 -O50 -8 1 -9 1 \
>   -f BlastTab genome_10 reads.fasta > results.txt 2>errors.log

I should add that for my case it was -I93 -J100.  The reads were only 
76bp and
it was common to have a few bp mismatches on the ends, hence 93% 
identity.  -J instead
of -Y because it was transcripts searching a reads database rather than 
the other way around.  80% is pretty low if the short sequences should 
be present 1:1 in the assembled genome, even for a highly polymorphic 
genome where only one haplotype might be present.


David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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