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### Picard ResortSam
sort -k1V $bowtieIndex.fa.dict_tmp > $bowtieIndex.dict
samtools view -h $bamFile | removeMultiMappers > ${bamBaseName}_mmf.tmp.bam
samtools index ${bamBaseName}_mmf.tmp.bam # because ReorderSam runs substantially faster if the input is an indexed BAM file.
picard ReorderSam I=${bamBaseName}_mmf.tmp.bam O=${bamBaseName}_mmf.bam REFERENCE=$bowtieIndex.fa
## samtools view -h $bamFile | removeMultiMappers | picard ReorderSam I=/dev/stdin O=${bamBaseName}_mmf.bam REFERENCE=$bowtieIndex.fa
samtools index ${bamBaseName}_mmf.bam
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## extract chromosome from bam file
samtools view -bo test.bam /home/brandl/mnt/chip-seq_study/ChIPSeq_February_2014/alignments_trimmed_nomulti_pooled/H2Az.bam 1
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## macs2 playground
macs2 -n --broad --gsize
#macs2 -n --gsize
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### deeptools
## https://github.com/fidelram/deepTools/wiki/All-command-line-options#bamCorrelate
#bamCorrelate bins --bamfiles $bamFiles --region 10:1:100000 --plotFile="bam_correlation.png" --numberOfProcessors=4 --corMethod spearman
## see how well bam files correlate using untrimmed data
bamCorrelate bins --bamfiles $bamFiles --plotFile="bam_correlation_untrimmed.png" --numberOfProcessors=4 --corMethod spearman
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### Peak calling with SPP
Rscript /home/brandl/bin/phantompeakqualtools/run_spp.R -c="../alignments_untrimmed/H2Az_Rep1_Lane2_Lib4454.0001.bam" -savp -out="test.txt"
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### other qc
## http://www.nature.com/nmeth/journal/v11/n1/full/nmeth.2786.html
# Teytelman et al. discovered that highly expressed loci were always enriched in ChIP peaks, regardless of which protein was pulled dow
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#### CHANCE
mcdir $baseDir/qc_chance
## convert example to sam format
bamToBed -i $baseDir/alignments_trimmed/H2Az_Rep1_Lane1_Lib4454_ca.bam > H2Az_Rep1_Lane1_Lib4454_ca.bed
samtools view -h -o H2Az_Rep1_Lane1_Lib4454_ca.sam $baseDir/alignments_trimmed/H2Az_Rep1_Lane1_Lib4454_ca.bam
/local/home/henry/bin/CHANCE/run_chance_linux.sh /usr/local/MATLAB/MATLAB_Compiler_Runtime/v717/
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## Use phantompeakqualtools to calculate quality tag (strand cross-correlation of peak)
# did the antibody-treatment enrich sufficiently so that the ChIP signal can be separated from the background signal?
## --> use https://code.google.com/p/phantompeakqualtools/
mcdir $baseDir/qc_phantompeaks
#Rscript /local/home/brandl/bin/phantompeakqualtools/run_spp.R
#Rscript run_spp.R <bamfile> -savp -out=<outfile>
ctrlBam=$baseDir/alignments_untrimmed/H3-3_Rep1_Lane1_Lib4453.bam
#DEBUG ctrlBam=$baseDir/alignments_untrimmed/H3K4me3_Rep2_Lane2_Lib4455.bam
Rscript /projects/bioinfo/holger/bin/phantompeakqualtools/run_spp.R
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for bamFile in $baseDir/alignments_untrimmed/*bam ; do
echo "processing $bamFile..."
# Rscript /home/brandl/bin/phantompeakqualtools/run_spp.R -c=$bamFile -savp -ou t=$(basename $bamFile).pt.log
## one output file is enough because output is tabular including inpuyt file name
# Rscript /home/brandl/bin/phantompeakqualtools/run_spp.R -c=$bamFile -i=$ctrlBam -savp -savd -odir=$(pwd) -out=phantom_qc.txt
## with control
# ( Rscript /home/brandl/bin/phantompeakqualtools/run_spp.R -c=$bamFile -savp -savd -odir=$(pwd) -out=phantom_qc_noctrl.txt &> $(basename $bamFile).pt.log ) &
## without control
# ( Rscript /home/brandl/bin/phantompeakqualtools/run_spp.R -c=$bamFile -savp -savd -odir=$(pwd) -out=phantom_qc_noctrl.txt &> $(basename $bamFile).pt.log ) &
done
wait
## todo visualize results
#phantom output format
#format:Filename<tab>numReads<tab>estFragLen<tab>corr_estFragLen<tab>PhantomPeak<tab>corr_phantomPeak<tab>argmin_corr<tab>min_corr<tab>Normalized SCC (NSC)<tab>Relative SCC (RSC)<tab>QualityTag)
mailme "phantom qc done"
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### motifs
## run meme-chip
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### profiles
## try deepTools
## differential binding diffbind