Intergenic annotation

Question

[Muhammad]

i use this command to give gene names in my bed file

bed_annotation INPUT.bed -g hg38 -o OUTPUT.bed 

the link of website is here : https://github.com/vladsavelyev/bed_annotation ant this is the output

chr1    29225   29244   WASH7P          -       4|CCTC
chr1    29747   29778   MIR1302-2       1       +       5|CCCCG
chr1    30855   30963   MIR1302-2               +       2|CT
chr1    32678   32692   .               .       5|CCTGA
chr1    32863   32873   .               .       5|GAAGG
chr1    33988   33999   .               .       6|CATGTG
chr1    34932   34940   FAM138A 3       -       3|CTG
chr1    34939   34945   FAM138A 3       -       3|TGA
chr1    34966   34977   FAM138A 3       -       4|CAGG
chr1    36862   36873   .               .       6|GGGGTG
chr1    36975   36986   .               .       4|TGCG

now for the remaning regions i want to do annotate with intergenic regions. so, i created intergenic file using

gunzip -c gencode/gencode.v43.annotation.sort.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' |bedtools sort -g hg38.genome |  bedtools complement -i stdin -g hg38.genome | gzip > my_intergenic.bed.gz

chr1    0       11868
chr1    31109   34553
chr1    36081   52472
chr1    53312   57597
chr1    64116   65418

it looks like this is my output correct? also i want to define these regions like any labelling any suggestion what can be done? Thank You

[lieven.sterck]

hi Muhammad

To keep your posts readable we advice to make use of the code-formatting option wherever possible, it's the 101010 button on the top op the edit box. I've done it for you this time.