I have one bed file with start and end coordinate (range in bed format). I need to extract a specific position from this range bed (for example I need to extract "chr12 25392999" position from the below bed file). How can I do that? could you anyone please help? Appreciate your help! Thanks in advance!
my example bed file looks like this ------>
chr12 25392977 25393116 KRAS_Intron2_Amp7
•
written
by
LionisOne •
awk -F '\t' '($1=="chr12" && int($2)<= 25392999 && 25392999 <= int($3))'
adjust < , and <= according to : Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
or
index your bed with tabix and
tabix your.bed.gz "chr12:25392999-25392999"
or
convert your query to bed and
bedtools intersect -wa -u -a database.bed -b query.bed
@Pierre Lindenbaum Thanks a lot! Its a great help! I will check and let you know.
Hi pierre.peterlongo, Thanks a lot for your help. It is really helpful. Really sorry, I was in vacation, after that, completely forgot to check your answer.
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And I'm still not Pierre Peterlongo (hi )
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