Generate BED file

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10 months ago

daffodil ▴ 10

Hi,

My goal is to generate a BED file that includes chr, the name of the gene, the start and end, the score, as well as the strand of the gene. Could you please guide me on how to take this data and generate a bed file?

Best regards

bed • 837 views

ADD COMMENT • link 10 months ago by daffodil ▴ 10

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Which organism you want to create a bed file for? Do you have the annotations for the attributes you need? What have you tried, and where did you get stuck?

ADD REPLY • link 10 months ago by barslmn ★ 2.3k

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without more context or explanation :

echo -e 'chr1\t11868\t14409\tDDX11L1\t0\t-' > out.bed

ADD REPLY • link 10 months ago by Pierre Lindenbaum 164k

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I want to creat bed file from mouce (mm10). I don't have the annotation. Should I have to get that? and from where? I really I am not familiar with that. It would be appritiated if you could guide me ? should I take them from UCSC?

ADD REPLY • link 10 months ago by daffodil ▴ 10

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use https://genome.ucsc.edu/cgi-bin/hgTables with mm10,

ADD REPLY • link 10 months ago by Pierre Lindenbaum 164k

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Thank you so much for your response. I have downloded the file but I have a question how i can change the name of gene from NCBI (NM_12344) to gene symbols?

ADD REPLY • link 10 months ago by daffodil ▴ 10

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