how to annotate chromosome position with the gene list file
Hello All,
I have chromosome position file which was obtained as a result of a CNV tool, which looks like: (file1)
chr1 11167376 11167465 amp
chr1 11167466 11167565 amp
chr1 11167566 11167598 neutral
chr1 11167599 11167644 del
chr1 11168123 11168180 amp
chr1 11168181 11168209 neutral
chr1 11168210 11168309 amp
chr1 11168310 11168409 amp
chr1 11168417 11168433 amp
chr1 11169248 11169336 amp
chr1 11169337 11169436 amp
chr1 11169437 11169487 amp
chr1 11169489 11169560 amp
chr1 11169562 11169649 amp
chr1 11169670 11169769 amp
chr1 11169770 11169806 amp
and I have a gene list file from UCSC: (file2)
chr1 11159886 11159888 EXOSC10
chr1 11166588 11167557 MTOR
chr1 11167542 11167544 MTOR
chr1 11167545 11167557 MTOR
chr1 11168238 11168343 MTOR
chr1 11168238 11168343 MTOR
chr1 11169347 11169427 MTOR
chr1 11169347 11169427 MTOR
chr1 11169706 11169786 MTOR
chr1 11169706 11169786 MTOR
chr1 11172909 11172974 MTOR
chr1 11172909 11172974 MTOR
chr1 11174375 11174510 MTOR
chr1 11174375 11174510 MTOR
I tried bedtools and bedops but it annotates many intermediate regions, my expected output is:
chr1 11167376 11167465 amp MTOR
chr1 11167466 11167565 amp MTOR
chr1 11167566 11167598 neutral MTOR
chr1 11167599 11167644 del MTOR
chr1 11168123 11168180 amp MTOR
chr1 11168181 11168209 neutral MTOR
chr1 11168210 11168309 amp MTOR
chr1 11168310 11168409 amp MTOR
chr1 11168417 11168433 amp MTOR
chr1 11169248 11169336 amp MTOR
chr1 11169337 11169436 amp MTOR
chr1 11169437 11169487 amp MTOR
chr1 11169489 11169560 amp MTOR
chr1 11169562 11169649 amp MTOR
chr1 11169670 11169769 amp MTOR
chr1 11169770 11169806 amp MTOR
So basically I want to annotate genes from file2 on file1, Thank you
1 answer
Hi, I am usually using syntax like this:
bedtools intersect -a file1 -b file2 -wao | awk -v OFS="\t" '{if($5 == ".") print $1,$2,$3,$4"_no_intersect"; else print $1,$2,$3,$4"_"$8}' | sort | uniq
Your files need to be tab separate. In your files it looks, that some regions are not intersect.
Output is:
chr1 11167376 11167465 amp_MTOR
chr1 11167466 11167565 amp_MTOR
chr1 11167566 11167598 neutral_no_intersect
chr1 11167599 11167644 del_no_intersect
chr1 11168123 11168180 amp_no_intersect
chr1 11168181 11168209 neutral_no_intersect
chr1 11168210 11168309 amp_MTOR
chr1 11168310 11168409 amp_MTOR
chr1 11168417 11168433 amp_no_intersect
chr1 11169248 11169336 amp_no_intersect
chr1 11169337 11169436 amp_MTOR
chr1 11169437 11169487 amp_no_intersect
chr1 11169489 11169560 amp_no_intersect
chr1 11169562 11169649 amp_no_intersect
chr1 11169670 11169769 amp_MTOR
chr1 11169770 11169806 amp_MTOR
EDIT: Also if you need in output just intersect regions, you can modify AWK script or make a pipe to grep -v "no_intersect"
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This looks like a bedtools intersect problem. What command did you use?