Blind Mole Rat

[李梓锋Lee_ZiFung]

Hi，

     I can not find blind mole rat(Spalax) data in UCSC.But I have the whole genome sequencing data of the blind mole rat.How can I convert my WGS data into different chromosomes maf.gz file or axt.gz file.Like the file in this website,

”hgdownload.soe.ucsc.edu/goldenPath/mm10/vsHetGla2/axtNet” .

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[Daniel Schmelter]

Hello,

Thank you for writing to the Genome Browser with your question about creating a pairwise alignment to the mouse genome.

Running the whole genome alignments can be a somewhat complicated process. The most complete documentation on the topic can be found here:

http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto

Since you may want to create your own MAF and AXT files, you will need to use the program doBlatzChainsNets.pl, which requires 2bit and chrom.sizes input files. Generating these will require two additional utilities "faToTwoBit" and "faSizes -detailed". The pairwise MAF generation process is described in detail here:

http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl

This will also generate chain files that can be viewed as bigChain files (https://genome.ucsc.edu/goldenPath/help/bigChain.html). There are three different types of pairwise MAFs generated with different filtering methods depending on the sensitivity you want.
Full - keeps all of the alignments for highest coverage, for distant relatives
Reciprocal best - highest standards, where query and target are both the same best match, for moderate distance relatives or poorly assembled genome.
Syntenic - maximizes connections, evolutionarily based for close relatives with well-assembled genomes

You can read more about MAF and bigMaf formats here:

https://genome.ucsc.edu/FAQ/FAQformat.html#format5
https://genome.ucsc.edu/goldenPath/help/bigMaf.html

I hope this was helpful. If you have any more questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,
Daniel Schmelter
UCSC Genomics Institute

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