Chicken galGal4 Multiz Alignment and Conservation track

[賴勇志]

Hi,

 

The multiz alignment and conservation tracks are very helpful to analyze our ChIP-Seq data. May I know when UCSC will provide them for chicken galGal4 assembly? Besides, what species will be used to align with the chicken genome? Many thanks.

 

Gary

 

[Steve Heitner]

Hello, Gary.

Thank you for using the UCSC Genome Browser.  This is on our list of tracks to create, but unfortunately, we cannot provide a time estimate of when this might be done nor a list of species that will be included.  I’m sorry we can’t be more specific than that.

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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[賴勇志]

Hi Steve,

 

Thank you very much for your information. I totally understand that and very thank so many useful resources UCSC provided. Is it possible to let me know the commands with every option UCSC used to build the multiz alignment and conservation (by PhastCons and PhyloP) tracks, e.g. one example for TBA I used as below? I would like to build a truck with 12 species with chicken as the reference. In fact, I am a beginner of multiple genome alignemnet, any suggestion is very wellcome. Many thanks.

 

all_bz + F=chicken "(((((((chicken turkey) (budgerigar (zebrafinch groundfinch)) alligator) turtle) lizard) (mouse human)) frog) zebrafish)"

 

Gary

[Luvina Guruvadoo]

Hello Gary,

You can find the exact procedures we use to create tracks by looking through the make docs in our source tree at http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=tree;f=src/hg/makeDb/doc. You can take a look at /hg38/multiz20way.txt or doc/tarSyr2/multiz20way.txt as examples on how to run multiple alignments.

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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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[賴勇志]

Hi Luvina,

 

Thank you so much. This is very helpful.

 

Gary