3. UCSC Genome Browser Tutorial: BLAT

UCSC Genome Browser Tutorial
Video 3
A tutorial for BLAT, a search tool that maps nucleotide sequences to the human genome. Here I discuss:
--how to check PCR primers with BLAT
--how to visualize sequencing results with BLAT
--supplementary nucleotide abbreviations

[@danapeca]

I found all your tutorials on UCSC Genome Browser very useful. Thanks Sam!

[@samallon9492]

+Loredana Peca Glad I could help, Loredana. Best of luck in all of your scientific endeavors!

[@semb12]

Hi Sam. Thanks a lot for posting this video - it really helped me with an assignment.

[@b0b0pizza]

thanks sam

[@taniadas3301]

Can I use blat to find exactly to which exons of a gene a probe sequence maps

[@malearimond5805]

Hi Sam, I watched your video and it was super helpful! Thank you very much! You also talked about the algorithm behind BLAT in the video, do you have more information about it? I have to write a paper on BLAT but haven't found any good papers yet.
Thanks in advance.
Kind regards
Male

[@minxie2210]

Thanks Sam. Can BLAT search for primers designed for the bisulfite converted sequences?

[@HimeBaezChan]

To BLAT the reverse primer you used the reverse sequence or reverse complementary?

[@samallon9492]

Reverse complement because BLAT expects all input sequences to be 5' -> 3'. Hope this helps!

[@HimeBaezChan]

@@samallon9492 It did. Im working on this right now. Thanks!

[@farhashazmeen5469]

can UCSC genome browser used to see the change in distribution of reads
at different labeling times with annotation?

[@samallon9492]

+Farha shazmeen Hey Farha! It sounds like you want to upload a custom track for that task. Did you check out my 4th video? That might put you on the right track (no pun intended). Good luck!