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;