Dinh/Dinh 2012/NOTES/2012-2-13: Difference between revisions
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cat normalized.BED >> normalized.R.cac.BED | cat normalized.BED >> normalized.R.cac.BED | ||
done >> log.Rcac | done >> log.Rcac | ||
* repeat this for all the samples. | |||
* Peak calling using FindPeak 4.0. The reason why MACS1.4 wouldn't work because MACS14 "shifts" read toward the center when reads are pileup on the forward strand and reverse strand. This shifting model wouldn't work for finding enrichment of certain regions in the genome (unlike motif finding, the size of the region is unknown and may be very large). | * Peak calling using FindPeak 4.0. The reason why MACS1.4 wouldn't work because MACS14 "shifts" read toward the center when reads are pileup on the forward strand and reverse strand. This shifting model wouldn't work for finding enrichment of certain regions in the genome (unlike motif finding, the size of the region is unknown and may be very large). | ||
for f in normalized.*BED | for f in normalized.*BED |
Revision as of 00:19, 15 February 2012
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) File:RemoveOverlapping.txt
- 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
- Strand specific normalization with both IgG and Input controls. Normalization of read depth is taken care of by regression model.
for chr in chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX chrY chrM do ./getCHR.pl $chr < Indx1.BED | sort -k2,3n > treat.BED ./getCHR.pl $chr < Indx7.BED | sort -k2,3n > input.BED ./getCHR.pl $chr < Indx4.BED | sort -k2,3n > iggcl.BED ftumch2 -i treat.BED -c input.BED iggcl.BED -o normalized.BED -rl 350 -cs 100000 -ws 5 -iv 5 cat normalized.BED >> normalized.R.cac.BED done >> log.Rcac * repeat this for all the samples.
- Peak calling using FindPeak 4.0. The reason why MACS1.4 wouldn't work because MACS14 "shifts" read toward the center when reads are pileup on the forward strand and reverse strand. This shifting model wouldn't work for finding enrichment of certain regions in the genome (unlike motif finding, the size of the region is unknown and may be very large).
for f in normalized.*BED do awk '{print $1"\t"$2"\t"$3"\t"$4"\t0\t"$6}' $f > tmp java -Xmx2G -jar /usr/local/fp4/FindPeaks.jar -input tmp -aligner bed -output . -wig_step_size 1 - dist_type 0 350 -subpeaks 0.5 -landerwaterman 0.001 -name $f -one_per done;