Question: Bed_intersect -s empty output
0
gravatar for mileti.enrichetta
4.9 years ago by
European Union
mileti.enrichetta0 wrote:

Hi!,

I have problems with bedintersect.

I need to intersect two bed files like these:

A.bed

 

chr1    10568    10571    -    5
chr1    10568    10571    -    5
chr1    10568    10571    -    5
chr1    10568    10571    -    5
chr1    11804    11900    +    2
chr1    11804    11900    +    2
chr1    11804    11900    +    2
chr1    11804    11900    +    2
chr1    16720    16745    +    2
chr1    16720    16745    +    2


B.bed

chr1    11373    12727    NR_046018    DDX11L1    +    Ex1*
chr1    11873    12227    NR_046018    DDX11L1    +    Ex1
chr1    12112    13221    NR_046018    DDX11L1    +    Ex2*
chr1    12227    12612    NR_046018    DDX11L1    +    In
chr1    12612    12721    NR_046018    DDX11L1    +    Ex2
chr1    12720    14909    NR_046018    DDX11L1    +    Ex3Last*
chr1    12721    13220    NR_046018    DDX11L1    +    In

if I run this line:

intersectBed -a A.bed -b B.bed -s -c >out

it return an empty file; If I run:

intersectBed -a A.bed -b B.bed  -c >out

it return a file with the overlapping coordinates.

Any suggestions for this problem?

bedtools software error • 1.2k views
ADD COMMENTlink modified 3.3 years ago by Biostar ♦♦ 20 • written 4.9 years ago by mileti.enrichetta0
0
gravatar for Aaronquinlan
4.9 years ago by
Aaronquinlan11k
United States
Aaronquinlan11k wrote:

The strand is expected to be in the 6th column for BED format. Your first file violates that rule. Use awk or perl to add two dummy columns this placing the strand in the 6th column.

ADD COMMENTlink written 4.9 years ago by Aaronquinlan11k

I try this, but it does not work!

ADD REPLYlink written 4.9 years ago by mileti.enrichetta0

Can you show what your A.bed file looks like after you have corrected the file such that the strand is the 6th column?

ADD REPLYlink written 4.9 years ago by Aaronquinlan11k
0
gravatar for mileti.enrichetta
4.9 years ago by
European Union
mileti.enrichetta0 wrote:

I try this, but it does not work!

ADD COMMENTlink written 4.9 years ago by mileti.enrichetta0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 900 users visited in the last hour