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Question: Genome file for Bam to Bed or Genome Coverage
0
gravatar for jlocker
2.6 years ago by
jlocker • 0
United States
jlocker • 0 wrote:

I generated BAM (mm9) files in Tophat and tried to convert them to Bedgraphs using the BedTools program. This program now requires a genome file (BamtoBed also requires this), which is different from the last time I used the program. Is an mm9 file available on Galaxy, or do I have to upload it. If I do upload, what is the required format?

Thanks,

Joe Locker
bedtools • 1.7k views
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modified 2.6 years ago • written 2.6 years ago by jlocker • 0
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gravatar for Mo Heydarian
2.6 years ago by
Mo Heydarian ♦ 830
United States
Mo Heydarian ♦ 830 wrote:

Hi Joe,

See this post from last week about the Genome file: bedTools - Genome file

The example Genome file in that post is the Genome file for mm9.

ADD COMMENT • link written 2.6 years ago by Mo Heydarian ♦ 830
1

For others reading, if you need this data for any genome that is at UCSC (http://genome.ucsc.edu), it can be extracted from the Table Browser with the "Get Data: UCSC Main" tool. Set "group" to "All Tables", "table" to "chromInfo", and "output format" to "all fields from selected table".

chromInfo from UCSC

ADD REPLY • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for jlocker
2.6 years ago by
jlocker • 0
United States
jlocker • 0 wrote:

Thanks. that was easy and fixed everything.
ADD COMMENT • link written 2.6 years ago by jlocker • 0
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