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