Question: Coverting Embl Format To Bed Format
0
gravatar for bioinfo
6.7 years ago by
bioinfo690
EU
bioinfo690 wrote:

I have an embl file of my annotated genome. How can I convert it to bed format so I can use it in Bed tools? Will I get the output like that in the converted bed file from embl? e.g.

Gene     start      end 
BRCA      120       279
BRCB      390       578
CDRA      890       1176
format • 2.2k views
ADD COMMENTlink modified 6.7 years ago by Istvan Albert ♦♦ 80k • written 6.7 years ago by bioinfo690
2
gravatar for Istvan Albert
6.7 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

Try ReadSeq http://www.ebi.ac.uk/cgi-bin/readseq.cgi

EDIT:

indeed ReadSeq does not convert to BED. Well then just convert to GFF then convert that to BED, see this perhaps

http://www.biostars.org/post/show/2/how-do-i-convert-from-bed-format-to-gff-format/

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Istvan Albert ♦♦ 80k

had a look before but there is no option to convert in Bed format

ADD REPLYlink written 6.7 years ago by bioinfo690

I guess you would need to convert GFF to BED then. Ah ... I just remembered that converting BED to GFF was the first question that I posted on Biostar: http://www.biostars.org/post/show/2/how-do-i-convert-from-bed-format-to-gff-format/

ADD REPLYlink written 6.7 years ago by Istvan Albert ♦♦ 80k

thanks..I am going through it

ADD REPLYlink written 6.7 years ago by bioinfo690

I managed to convert my embl format to C++ text format..now I m trying to convert that to bed

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by bioinfo690
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