Format of HotSpot file
Huimin Kang
To whom it may concern,
I wanted to get recombination hotspots in human genome and downloaded decodeHotSpotFemale.txt.gz from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/. However, I don’t know the format of this file. I guess the second, third and fourth columns are chromosome, start position (0-based) and end position (1-based), respectively. The last column is possibly recombination rate, but I don’t know what does the first column mean. Could you tell me the format of this file? And do these hotspots can be applied in genomes from 1000 Genomes Project?
Thank you!
Sincerely,
Huimin Kang
Jairo Navarro Gonzalez
Hello Huimin,
Thank you for using the UCSC Genome Browser and your question about the file format for decodeHotSpotFemale.txt.gz.
This file is part of the deCODE Recombination map track for hg19 and the decodeHotSpotFemale.txt.gz is the underlying data file for the Hot Spot Female sub-track. Clicking the schema button, you can view what each column represents. From this page, the first column represents the bin field which is used by the Genome Browser for performance efficiency. You can remove this column using the following 'awk' command.
awk '{print $2, $3, $4, $5}' decodeHotSpotFemale.txt > myNewFile.txt
You can learn more about this file and how it can be applied for genomic analysis from the track description page. For example:
There are also tracks depicting the difference between male and female recombination rates, and a track showing recombination hotspots (i.e., bins with standardized recombination rates higher than 10).
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.
Jairo Navarro
UCSC Genomics Institute
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