Generate BED file

0

Entering edit mode

9 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 • 830 views

ADD COMMENT • link 9 months ago by daffodil ▴ 10

1

Entering edit mode

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 9 months ago by barslmn ★ 2.3k

1

Entering edit mode

without more context or explanation :

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

ADD REPLY • link 9 months ago by Pierre Lindenbaum 164k

0

Entering edit mode

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 9 months ago by daffodil ▴ 10

3

Entering edit mode

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

ADD REPLY • link 9 months ago by Pierre Lindenbaum 164k

0

Entering edit mode

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 9 months ago by daffodil ▴ 10

Login before adding your answer.