BLAT function in Web version ? - Help :)

[Hania Czerwinska]

Hi all,

In the downloadable version, I can BLAT a sequence to find the location using the Tools dropdown.

Tools >Blat seems to have disappeared from the Online version. Can anyone help? I need to  do this urgently for a class of students

Thanks so much :)

Hania

[igv-help]

Hi Hania,

In the IGV-Web app you can BLAT the following:

- if you right-click on a read in a BAM track, you can select 'BLAT read sequence' from the popup menu.

- if you zoom into a sufficiently small region of the genome you can right click on the sequence track and select to  BLAT the reference sequence of that region. The menu item currently says "BLAT read sequence", but it should say "BLAT visible sequence" - which is what the action does. You need be zoomed in because there's a limit to how long a sequence can be sent to the BLAT function.

Helga

[igv-help]

Update - I've added an experimental BLAT item under a new "Tools" menu similiar to IGV desktop.   You can access this from

https://igv.org/app-test

I don't have an ETA on when this feature will be released, but please give app-test a try and see if it has what you need for your class.   A caveat,  I haven't been able to test this completely as the UCSC genome browser, where BLAT searches are performed, is down this evening.   I presume they will have the server up soon.

IGV-Web and IGV desktop are distinct software development efforts.  IGV-Web implements many but not all of IGV Desktop features.