UCSC In-Silico PCR

[Tongyao Wang]

Hello,

I see there are several kinds of chrom files in your database. Besides the normal files, like "chr1.fa", there are also the "alt", "random", and "chrUn". So when the website run the in-silico PCR, which kind of files do you use? Only the normal ones, or all the files? Thank you.

Thanks,

Tongyao

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Tongyao Wang

Bioinformatics

College of Science

Northeastern University

wan...@husky.neu.edu

860-617-0735

[Matthew Speir]

Hi Tongyao,

Thank you for your question about the In-Silico PCR tool at the UCSC Genome Browser. The In-Silico PCR tool uses a 2bit file, which is a compressed binary file that contains the entire genome sequence, including the standard chromosomes, "alt", "random", and "chrUn" sequences. You can find more information on the 2bit format on the following help page: http://genome.ucsc.edu/FAQ/FAQformat.html#format7. You can find the 2bit files for the assembly of your choice on our download server, http://hgdownload.soe.ucsc.edu/downloads.html, under the "Full data set" link for that assembly.

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

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[Tongyao Wang]

Thank you, Matthew. If I understand it correctly, I can directly use the 2bit file to run the isPcr program locally after download it? And will the isPcr run faster with the 2bit file than the regular chromosome file with all the genome sequence?

Thanks,

Tongyao

[Steve Heitner]

Hello, Tongyao.

The isPcr command line states:

usage:
       isPcr database query output
where database is a fasta, nib, or twoBit file or a text file containing
a list of these files,  query is a text file file containing three columns: name,
forward primer, and reverse primer,  and output is where the results go.
The names 'stdin' and 'stdout' can be used as file names to make using the
program in pipes easier.

So yes, you can definitely use 2bit files to run isPcr.  It is faster to use 2bit files as opposed to FASTA files, but the speed difference would probably be hardly noticeable.  The real benefit of using 2bit over FASTA is the fact that the 2bit file is a single all-inclusive file that negates the need to download and keep track of a large number of individual FASTA files.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  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.

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Steve Heitner
UCSC Genome Bioinformatics Group

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