Blat returning duplicate entries

Question

[picy2k]

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 reads
• outputFile: the results contain duplicated entries.

Could anyone explain if this is a result of the algorithm or a bug?

[Ram]

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.

[picy2k]

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)

[Ram]

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.

[Phil S.]

can you elaborate on what you mean with 'duplicate entries'? A query listed two or even more times?

[picy2k]

eg blast8 output i got

gDNAHWI-ST884_106:1:1101:5458:3416#0/1  contig00634     100.00  101     0       0       1       101     348     248     3.4e-51 199.0
gDNAHWI-ST884_106:1:1101:5458:3416#0/1  contig01077     100.00  50      0       0       1       50      48      97      4.8e-21 99.0
gDNAHWI-ST884_106:1:1101:5458:3416#0/1  contig00634     100.00  101     0       0       1       101     348     248     3.4e-51 199.0
gDNAHWI-ST884_106:1:1101:5458:3416#0/1  contig01077     100.00  50      0       0       1       50      48      97      4.8e-21 99.0

as you can see, for this output and for this read, i received 2 duplicates

[Sean Davis]

Have you checked to see that you do not have the same read in the fasta file twice?

Answer 1

[picy2k]

Repeated reads in the reads.fa problem.