Colourful BLAT visualisation to track

[Darya Vanichkina]

Hi,

How do I save the “colourful” visualisations that BLAT generates for aligned/unaligned regions/bases to a custom track?

I have followed the instructions here:

https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/u6UmVz06Mis

on how to convert the BLAT output to a psl, but the colours for mismatches/indels are not preserved. Is there a way I can get these out?

Thanks in advance,
Darya

[Matthew Speir]

Hi Darya,

Thank you for your question about maintaining the BLAT alignment track coloring in a custom track.

The instructions provided in that answer will produce a custom track that contains only the regions that were cover by the resulting BLAT hits. As you noted, this is because you are converting your PSL alignment into a bigBed file that is absent of the match/mismatch/etc. information.

We have a format that is currently under development called bigPsl that will provide you with the display you are interested in. There is no official documentation currently for this format, but support exists for in the Genome Browser. We hope to have this documentation available sometime in the future. Here is a set of instructions that you can use to create a bigPsl custom track from your PSL results:

1. Save the results of your BLAT search to a file as indicated in steps 1 and 2 of this previous mailing list question: https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/u6UmVz06Mis

2. Take the sequences that you used to create those BLAT results and place them in a FASTA formatted file. You can more on the FASTA format here: http://genetics.bwh.harvard.edu/pph/FASTA.html. Ensure that the sequence names used in your FASTA file are the same as those in the qName (column 10) field of the PSL file of your BLAT results.

3. Download the utilities pslToBigPsl and bedToBigBed from our downloads server: http://hgdownload.soe.ucsc.edu/admin/exe/

4. Run the pslToBigPsl to create your bigPsl file:
   
    pslToBigPsl -fa=yourFastaFile.fa yourBlatResults.psl stdout | sort -k1,1 -k2,2n > yourBlatResults.bigPslInput

Here, "yourFastaFile.fa" is the FASTA file you created in step 2 and "yourBlatResults.psl" is the file you created in step 1.

5. Next convert this bigPsl file into a special bigBed file for loading as a custom track. This will be a special bigBed file that will contain all of the information needed to display the matches/mismatches/etc. You can use the following command to carry out this conversion:

    bedToBigBed -type=bed12+12 -tab -as=bigPsl.as yourBlatResults.bigPslInput chrom.sizes myBigPsl.bb

Here "yourBlatResults.bigPslInput" is the file you created in step 4. The chrom.sizes file for mm10 can be found here: http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.chrom.sizes. I've also attached the bigPsl.as file you will need for this step to this email.

6. Lastly, upload your custom track to the Genome Browser. You can use something like the following track line to do so:
   
    track name="BLAT Results" description="BLAT Results in bigPsl Format" type=bigPsl bigDataUrl=http://yoursite/path/to/file/myBigPsl.bb

Here "myBigPsl.bb" is the file you created in step 5. Note that even though we've created a bigBed file, the "type=bigPsl" in the track line is what tells the browser to interpret and display the file as a PSL.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group