a.bed looks like this:
chr1 631977 631979 -2.777777778
chr1 631994 631996 31.5625
......
b.bed looks like this:
chr1 11873 11874 DDX11L1 0 +
chr1 17435 17436 MIR6859-3 0 -
......
After I ran:
closestBed -a a.bed -b b.bed -D b > c.bed
c.bed looks like this:
chr1 631977 631979 -2.777777778 . -1 -1 . -1 . -1
chr1 631994 631996 31.5625 . -1 -1 . -1 . -1
......
Both a & b were formatted using galaxy before running. Help!
3 answers
It gave me this result when I ran your example:
chr1 631977 631979 -2.777777778 chr1 17435 17436 MIR6859-3 0 - -614542 chr1 631994 631996 31.5625 chr1 17435 17436 MIR6859-3 0 - -614559
Check that the files are tab-delimeted, there is something wrong with formatting. It should work.
Try 3 things:
1) Instead of:
closestBed -a a.bed -b b.bed -D b > c.bed
use
closestBed -a a.bed -b b.bed -D "b" > c.bed
2) Check that your file is formatted properly (are marina suggested):
head a.bed
head b.bed
if you don't get something like what you put above then do:
cat a.bed | tr '\r' '\n' > a_v2.bed #removes carriage returns and makes a new line
or if it's not tab delimited
cat a.bed | tr '--> x <--' '\t' #where --> x is your separator is, i.e. ' ' (space) ',' (comma) etc...
3) Sort the file
sort -k1,1 -k2,2n a.bed > a_sorted.bed
--->> EDIT <<---
I just copy/pasted your input which looks like space delimited, I converted it to tab delimited:
cat a.bed | tr ' ' '\t' > a2.bed
cat b.bed | tr ' ' '\t' > b2.bed
then used closestBed:
closestBed -a a2.bed -b b2.bed -D "b"
which gave me
chr1 631977 631979 -2.777777778 chr1 17435 17436 MIR6859-3 0 - -614542
chr1 631994 631996 31.5625 chr1 17435 17436 MIR6859-3 0 - -614559
Thanks. It's solved.
The b.txt looks like
NM_001276352 chr1 - 67092175 67134971 C1orf141
NM_000299 chr1 + 201283451 201332993 PKP1
......
When I ran
cat b.txt | awk '{if($3 == "-") {print $2 "\t" $5-1 "\t" $5 "\t" "\t" "\t" $3} else {print $2 "\t" $4 "\t" $4+1 "\t" "\t" "\t" $3} }' > b.bed
The result was properly printed. But when I ran
cat b.txt | awk '{if($3 == "-") {print $2 "\t" $5-1 "\t" $5 "\t" $6 "\t" $1 "\t" $3} else {print $2 "\t" $4 "\t" $4+1 "\t" $6 "\t" $1 "\t" $3} }' > b.bed
The last 2 columns went to second line for each original row
chr1 67134970 67134971 C1orf141
NM_001276352 -
chr1 201283451 201283452 PKP1
NM_000299 +
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Thanks guys. The spaces were inappropriately added by awk:
There were no spaces in
b.txt. Any suggestion?Can we have a snapshot of the
b.txtfile? You can edit your answer and add it there.No commas in awk (your script puts spaces (comma) and tabs but you need only tabs: