Question: How to include strand information in the result when running bedtools complement?
0
gravatar for biolab
4.3 years ago by
biolab1.1k
biolab1.1k wrote:

Hi everyone,

I am using bedtools complement to find the regions not covered in a GFF file.

Genome file is as follows.

chr1    12222

GFF file likes below.

chr1    db      exon    1       45      .       +       .       ID=gene1
chr1    db      exon    90      450     .       +       .       ID=gene2
chr1    db      exon    1       30      .       -       .       ID=gene99

I run complementBed -i <gff_file> -g <genome_file> and got the following result.

chr1    45      89
chr1    450     12222

This is not what I expected. I hope to get the following information, which includes strand symbol. Could anyone help?  Thank you very much!

chr1    45      89       +
chr1    450     12222    + 
chr1    30      12222    -

 

bedtools • 1.3k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by biolab1.1k
1
gravatar for iraun
4.3 years ago by
iraun3.5k
Norway
iraun3.5k wrote:

Sorry but this is the same question you asked some time ago?
problem with bedtools complement: how to extract strand information?

ADD COMMENTlink written 4.3 years ago by iraun3.5k

Hi airan, thank you for your comment.  Too bad memory I have :)   I will separate the strands and then do bedtools. 

ADD REPLYlink written 4.3 years ago by biolab1.1k

No problem :)

ADD REPLYlink written 4.3 years ago by iraun3.5k
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