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.
Regards, David Mathog [email protected] Manager, Sequence Analysis Facility, Biology Division, Caltech _______________________________________________ EMBOSS mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/emboss
