Question: How To Perform An Exhaustive Search (Report All Hits) Using Blat
gravatar for Shaojiang Cai
7.3 years ago by
Shaojiang Cai100
Shaojiang Cai100 wrote:

I am using Blat to map long contigs to annotated transcripts. But Blat does not report all feasible hits exhaustively. For example, there is a transcript T with length 2280. If I aligned all contigs to it, Blat reports one hit with range [770, 2280]:

Transcript T:   ===============================================================
Hit (contig A):                           -------------------------------------
                                          ^770                                ^2280
               |<-    missing region    <-|

But if I truncate the transcript (keep the first 770 bases only) and blat again, there is an exact hit: 770 matches, 0 mismatch, 0 gap.

Partial T:      ==========================
Hit (contig B): --------------------------
                ^0                       ^770                                                      
                |<-    An exact hit    <-|

Somehow Blat does not report Contig B at first (The missing region). This is not what I want.

I do not want to use Blast, because my program is all using Blat format.

I tried the options -fine and -oneOff=1 to do the same mapping, but the results are the same.

Does anybody know how to enforce exhaustive searching using Blat? Or any script to convert blastn results to PSL format? Thanks.

alignment mapping blat • 2.1k views
ADD COMMENTlink modified 7.3 years ago • written 7.3 years ago by Shaojiang Cai100

I don't understand the question. It is not clear from your description what are the differences in the results that you are getting.

ADD REPLYlink written 7.3 years ago by Istvan Albert ♦♦ 84k

@istvan_albert modified. Please help

ADD REPLYlink written 7.3 years ago by Shaojiang Cai100

Sounds like it might be a multiple hit issue. Please post the raw psl output to your question.

ADD REPLYlink written 7.3 years ago by Jeremy Leipzig19k
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