repeatmasker alignment

[Matthew BOROK]

Hello,

My name is Matthew Borok and I am a postdoc working in Creteil, France. I am interested in analyzing transposon expression in some datasets, but I have had trouble finding a file of alignments to the human genome. I did the same analysis on mouse samples with an alignment file titled [UCSC_Main_on_Mouse__rmskAlignBaseline_(genome)].gtf Does the equivalent file for the human genome exist and could you please let me know how to find it? Thanks very much and have a nice day.

Best regards,

Matthew Borok

 

 

[Matthew Speir]

Hello, Matthew.

Thank you for your question about obtaining RepeatMasker data from the UCSC Genome Browser.

We provide RepeatMasker data in a two different formats:

• https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.align.gz

hg38.fa.align.gz - RepeatMasker .align file. RepeatMasker was run with the
-s (sensitive) setting.
June 20 2013 (open-4-0-3) version of RepeatMasker
RepBase library: RELEASE 20130422

• https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.out.gz

hg38.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
June 20 2013 (open-4-0-3) version of RepeatMasker
RepBase library: RELEASE 20130422

You can also use the Table Browser to obtain a GTF of the data using the following steps:

1. Go to https://genome.ucsc.edu/cgi-bin/hgTables
2. Make the following selections under "Select Dataset"

clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: Repeats
track: RepeatMasker
table: rmsk

3. Under "Retrieve and display data", make these selections

output format: GTF - gene transfer format (limited)
output filename: enter a name, or leave blank to view results in your web browser.

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues? Host a workshop: http://bit.ly/ucscTraining

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Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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