Dinh/Dinh 2012/NOTES/2012-2-13

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Revision as of 22:54, 14 February 2012 by >Dinh (Created page with '==24 ChIP-seq - Stimulated and Resting Neurons== *Analysis at repeats. Downloaded RepeatMasker track fro mm9. Then filtered and get Non-overlapping windows: 2072 awk '{if($12…')
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24 ChIP-seq - Stimulated and Resting Neurons

  • Analysis at repeats.
Downloaded RepeatMasker track fro mm9. Then filtered and get Non-overlapping windows:
 2072  awk '{if($12 ~ /DNA/) print $0}' RepeatMasker_mm9.txt | ./getNonOverlapping.pl > DNA_repeats.nonoverlapping &
2073  awk '{if($12 ~ /LINE/) print $0}' RepeatMasker_mm9.txt | ./getNonOverlapping.pl > LINE_repeats.nonoverlapping &
2074  awk '{if($12 ~ /SINE/) print $0}' RepeatMasker_mm9.txt | ./getNonOverlapping.pl > SINE_repeats.nonoverlapping &
2075  awk '{if($12 ~ /LTR/) print $0}' RepeatMasker_mm9.txt | ./getNonOverlapping.pl > LTR_repeats.nonoverlapping &
2076  awk '{if($12 ~ /Satellite/) print $0}' RepeatMasker_mm9.txt | ./getNonOverlapping.pl > Satellite_repeats.nonoverlapping &
File:GetNonOverlapping.txt
  • Note that some repeat segments overlaps between these difference repeat class.
cat *_repeats.nonoverlapping | sort -k1,1 -k2,3n > sorted.Repeats (3,188,316 entries)
./removeOverlapping < sorted.Repeats > tmp
mv tmp sorted.Repeats (3,187,848 entries)
  • Remove chr*_random entries
awk '{if($1 !~ /_random/) print $0}' sorted.Repeats > sorted.Repeats_norandom
  • Final repeat regions file: 3,127,206 entries
Started with 3,188,316 non-overlapping entries for DNA, LINE, SINE, LTR, and Satellite repeats
Then removed entries/segments which have over-lapping labels -> 3,187,848 entries left
Then removed entries on chr*_random -> 3,127,206 entries -> Non-overlapping repeat regions