Blat returning duplicate entries
I observed using the flags: -fastMap with -minIdentity=100
$ blat -fastMap -minIdentity=100 -out=blast8 db.fa reads.fa outputFile
db.fa: fasta containing contigs from newbler assembly process.reads.fa: Hi-seq readsoutputFile: the results contain duplicated entries.
Could anyone explain if this is a result of the algorithm or a bug?
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Repeated reads in the reads.fa problem.
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Someone could explain if you were to provide more details and elaborate on your goal and your approach. Right now, the information given is so sparse that only you know what you're talking about.
Goal: I'm trying to map both gDNA and mRNA reads pre-binned into a ortholog group back onto contigs constructed from the same set of gDNA reads from before. (@Ram i don't see how specifying the goal is important in answering this but I've included since I need some insight from the community)
the approach is basically running blat from the command line (i've edited the post to include this)
can you elaborate on what you mean with 'duplicate entries'? A query listed two or even more times?
Have you checked to see that you do not have the same read in the fasta file twice?
Stating your goal serves to validate your approach. It also finds people that seek help with school assignments without investing any effort in it themselves.