Crassostrea Virginica genome

[Scott Riley]

Is there a way I can import the Crassostrea viriginica genome to your site to search for primer pairs that I have?

 

Thanks,

 

Scott Riley

 

Masters Student | Kelly Lab
Treasurer | BioGrads
Department of Biological Sciences
Louisiana State University
804-537-0544

 

[Cath Tyner]

Hello Scott,

Thank you for contacting the UCSC Genome Browser support team. Below are steps you can take to accomplish your goal:

1. You can obtain the sequence file: 

GCF_002022765.2_C_virginica-3.0_genomic.fna.gz

at 

ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/Crassostrea_virginica/all_assembly_versions/GCF_002022765.2_C_virginica-3.0/

2. Convert that fna.gz file to a "2bit" file by using one of our utilities: faToTwoBit

You can download your operating system specific utility here: http://hgdownload.soe.ucsc.edu/admin/exe/

3. You can run "faToTwoBit" on the command line to see the usage statement:

$ faToTwoBit

faToTwoBit - Convert DNA from fasta to 2bit format

usage:

   faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit

options:

   -long          use 64-bit offsets for index.   Allow for twoBit to contain more than 4Gb of sequence.

                  NOT COMPATIBLE WITH OLDER CODE.

   -noMask        Ignore lower-case masking in fa file.

   -stripVersion  Strip off version number after '.' for GenBank accessions.

   -ignoreDups    Convert first sequence only if there are duplicate sequence

                  names.  Use 'twoBitDup' to find duplicate sequences.

4. Once you have your 2bit file, you'll need to install the standalone "isPcr" program:

* http://www.kentinformatics.com/products.html

You will need to contact Kent Informatics directly to obtain this program:

* http://www.kentinformatics.com/contact-us.html

* Here is a related mailing list question about getting started with the "isPcr" program.

Please respond to this list if you have further questions!

Thank you for contacting the UCSC Genome Browser support team. 

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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