chain file request for bosTau7To UMD3.1

[Nuket, Bilgen]

Hi,

I have two problems…

1- In my data set I used bosTau7 build as my reference genome file. Now I need to lift over variant files to UMD3.1.

To achieve that I planned have to lift over from 7 to 4 and 4 to UMD3.1. 

Are you planning to make a chain file for bosTau7To UMD3.1 ?

2- how many bosTau7 genomes out there? I downloaded from http://support.illumina.com/sequencing/sequencing_software/igenome.html and I also use IGV whihc has bostau7 genome downloaded. But In the trying process of lifting over I realised that those file are not same. Should not they be the same?

I am very confused

Thank you

Bad input: the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference

                    

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[Steve Heitner]

Hello, Bilgen.

The liftOver files you refer to already exist:

bosTau7 to bosTau4/6: http://hgdownload.cse.ucsc.edu/goldenPath/bosTau7/liftOver/
bosTau4 to bosTau6: http://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/liftOver/

The UCSC bosTau7 assembly is based on the Baylor Btau_4.6.1 assembly.  There is only one Baylor Btau_4.6.1 assembly, but as with any assembly, several institutions have made it available on their sites and each institution has their own method of processing the raw data.  The Illumina web site you referred to has download files from Ensembl, NCBI and UCSC.  If you are intending to use the UCSC liftOver tool, I would recommend using the UCSC data wherever possible, but your query and target data should certainly be from the same institution.  One of the main differences between the UCSC data and the Ensembl/NCBI data is that UCSC chromosome names include “chr” (e.g., “chr1” versus just “1” for chromosome 1).  The UCSC liftOver utility requires chromosome names to include the “chr”, so it is best to just use the UCSC data 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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