Question: Genome file for Bam to Bed or Genome Coverage
0
gravatar for jlocker
2.1 years ago by
jlocker0
United States
jlocker0 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 • 1.2k views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by jlocker0
1
gravatar for Mo Heydarian
2.1 years ago by
Mo Heydarian790
United States
Mo Heydarian790 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 COMMENTlink written 2.1 years ago by Mo Heydarian790
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 REPLYlink written 2.1 years ago by Jennifer Hillman Jackson25k
0
gravatar for jlocker
2.1 years ago by
jlocker0
United States
jlocker0 wrote:

Thanks. that was easy and fixed everything.

ADD COMMENTlink written 2.1 years ago by jlocker0
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