Female dna Y?

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Question: Female dna Y?

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2.2 years ago by

irusk • 10

Canada

irusk • 10 wrote:

I wanted to ask you a question when you load a fasta and vcf file into blat, blast or galaxy programs do they automatically load a Y chromosome data into female sequences because of the similarities on the X chromosome?

canonical-female reference galaxy custom-genome • 639 views

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modified 2.1 years ago • written 2.2 years ago by irusk • 10

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2.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, the PAR region between the X and Y chromosome will capture the same hits.

Options:

These Y-chrom hits can be removed from the resulting BAM dataset before further analysis
Some genome indexed at http://usegalaxy.org have a "canonical female" genome build - use that
Create your own "canonical female" genome build as a Custom Reference genome. The modification is to remove the Y chromosome fasta sequence. https://wiki.galaxyproject.org/Support#Custom_reference_genome

Best, Jen, Galaxy team

ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

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2.1 years ago by

irusk • 10

Canada

irusk • 10 wrote:

Thanks Jennifer, I was referring to sry mutations and DELYq11 mutation, maybe turner mosiac? with Y

ADD COMMENT • link written 2.1 years ago by irusk • 10

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