bed file conversion and comparing with the genome to find its region

Question

[kapil.joshi036]

I have a bed file with the co-ordinates includes chr start and end columns.

#chr    start   end
chrM    1        1
chrM    2        2
chrM    3        3
chrM    4        4
chrM    5        5
chrM    7        7
chrM    8        8
chrM    9        9
chrM    10      10
chrM    11      11
chrM    12      12
chrM    13      13
chrM    14      14

here there are 2 region are present i want to get output like

#chr    start   end
 chrM   1        5
 chrM    7       14

which tool should i use to perform this after this i need to find its location into the mitochorial genome

Answer 1

[Pierre Lindenbaum]

I'm afraid your BED file only describes deletions because a BED in half-open : see chromEnd in https://genome.ucsc.edu/FAQ/FAQformat.html#format1

the tool you need is "bedtools merge" http://bedtools.readthedocs.io/en/latest/content/tools/merge.html

which tool should i use to perform this after this i need to find its location into the mitochorial genome

uh ???

[kapil.joshi036]

sir , actually i jst have the co-ordiantes of mitocondrial sequence so i wannt to find its location into the mitochondrial genome

[GenoMax]

If you have co-ordinates then aren't they the location in the genome?

[kapil.joshi036]

i found the solution for it download the mtDNA gene bed file and annotate with bedtools

Answer 2

[michael.ante]

Hi,

To merge a bed-file, just use bedtools merge.

bedtools merge -i my_file.bed > merged_file.bed

[EDIT] regarding your second question, you may want to have a look at bedtools annotate or bedtools closest.

Cheers,

Michael