Blat Programme

Question

[Dr.Mahantesha Naika B.N.]

Hi, I am new to BLAT. I am getting output without E value and percentage identity. Can anyone suggest how to add these two points in commond lines along with datatype and query? or suggest in any output format which provides these two parameters along with other parameters?

Thanks & regards, Mahantesha

Answer 1

[Pavel Senin]

Hi, I guess that these are not readily available and you will need to compute these numbers as indicated here, with a code sample

...
Question: "Using my own command-line Blat server, how can I replicate the percent identity and score calculations produced by web-based Blat?"

Response: There isn't an option to command-line Blat that gives you the percent ID and the score. Instead, you will have to write your own program to produce the calculations, incorporating some of the functions from the Genome Browser source code. ...

Answer 2

[Prakki Rama]

Change -out=blast8 while running blat, it should give the result you wanted.