I've produced a list of CNV(copy number variation) data like below:
chr10 10271614 10659796 DEL
chr10 107242905 107243436 DEL
chr10 107940570 107941687 DEL
chr10 108020235 108022638 DEL
chr10 111562017 111568300 DEL
chr10 116956782 117389734 DEL
chr10 117005207 117396827 DEL
Just wondering if we have any VISUALIZATION software (say to visualize them on genome browser) so that I can check if my CNVs are overlapped? Thanks
•
written
by
Bioscientist
convert your file to BED and upload it as a custom track in the UCSC genome browser.
Exactly. Select a color that is different from that used by the UCSC browser for other/known CNVs.
thanks a lot! cannot say enough thanks to you guys! always help me a lot
Pre-visualization, you could also use BEDTools mergeBed, something like:
mergeBed -n -i cnvs.bed > cnvs.overlap-counts.bed
where cnvs.bed is your CNV file and the final column in the output file will like the number of overlaps. So, you could get regions with more than a single CNV as:
awk '($5 > 1)' cnvs.overlap-counts.bed > overlapped.bed
Either way, IGV is also a very good tool for visualizing.
thanks a lot! cannot say enough thanks to you guys! always help me a lot
Agree with Pierre above. I've pasted an example you could use below.
track name=normal description="Normal (red=deletion, green=duplication)" visibility=4 priority=1 itemRgb="On"
chr1 696961 747786 12087_N_PC 140 . 0 0 255,0,0
chr6 26845010 26876548 12087_N_PC 260 . 0 0 128,0,0
track name=tumor description="Tumor (red=deletion, green=duplication)" visibility=4 priority=1 itemRgb="On"
chr18 67191847 67206726 12087_T_PC 0 . 67191847 67206726 0,128,0
chr20 54595851 55224865 12087_T_PC 0 . 54595851 55224865 0,128,0
If the file is not too large, you could use the file as-is, store them somewhere, and use its URL on http://gosling.js.org.
Log in to answer this question.
