Last updated: 2019-02-15

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Knit directory: threeprimeseq/analysis/

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    Modified:   analysis/28ind.peak.explore.Rmd
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    Modified:   analysis/pheno.leaf.comb.Rmd
    Modified:   analysis/pipeline_55Ind.Rmd
    Modified:   analysis/swarmPlots_QTLs.Rmd
    Modified:   analysis/test.max2.Rmd
    Modified:   analysis/test.smash.Rmd
    Modified:   analysis/understandPeaks.Rmd
    Modified:   code/Snakefile

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File Version Author Date Message
html bd7f203 Briana Mittleman 2018-07-09 Build site.
Rmd 4348871 Briana Mittleman 2018-07-09 call peaks on nuclear
html f4f1918 Briana Mittleman 2018-07-06 Build site.
Rmd 2522654 Briana Mittleman 2018-07-06 fix axis
html a0541e3 Briana Mittleman 2018-07-06 Build site.
Rmd df5cfe4 Briana Mittleman 2018-07-06 add Yangs peaks
html 9de3677 Briana Mittleman 2018-07-05 Build site.
Rmd c619183 Briana Mittleman 2018-07-05 examine long peaks
html 2d67ec5 Briana Mittleman 2018-07-05 Build site.
Rmd 15c7967 Briana Mittleman 2018-07-05 add split analysis
html 24c6663 Briana Mittleman 2018-07-03 Build site.
Rmd 776fc62 Briana Mittleman 2018-07-03 genome cov stats
html b48f27c Briana Mittleman 2018-07-02 Build site.
Rmd 1e2ff4c Briana Mittleman 2018-07-02 evaluate bedgraph regions

Create Bedgraph

I will call peaks de novo in the combined total and nuclear fraction 3’ Seq. The data is reletevely clean so I will start with regions that have continuous coverage. I will first create a bedgraph.

#!/bin/bash

#SBATCH --job-name=Tbedgraph
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=Tbedgraph.out
#SBATCH --error=Tbedgraph.err
#SBATCH --partition=broadwl
#SBATCH --mem=40G
#SBATCH --mail-type=END


module load Anaconda3
source activate three-prime-env 

samtools sort -o /project2/gilad/briana/threeprimeseq/data/macs2/TotalBamFiles.sort.bam /project2/gilad/briana/threeprimeseq/data/macs2/TotalBamFiles.bam

bedtools genomecov -ibam /project2/gilad/briana/threeprimeseq/data/macs2/TotalBamFiles.sort.bam -bga > /project2/gilad/briana/threeprimeseq/data/bedgraph/TotalBamFiles.bedgraph

Next I will create the file without the 0 places in the genome. I will be able to use this for the bedtools merge function.

awk '{if ($4 != 0) print}' TotalBamFiles.bedgraph >TotalBamFiles_no0.bedgraph 

I can merge the regions with consequtive reads using the bedtools merge function.

  • -i input bed

  • -c colomn to act on

  • -o collapse, print deliminated list of the counts from -c call

  • -delim “,”

This is the mergeBedgraph.sh script. It takes in the no 0 begraph filename without the path.

#!/bin/bash

#SBATCH --job-name=merge
#SBATCH --account=pi-yangili1
#SBATCH --time=8:00:00
#SBATCH --output=merge.out
#SBATCH --error=merge.err
#SBATCH --partition=broadwl
#SBATCH --mem=16G
#SBATCH --mail-type=END

module load Anaconda3
source activate three-prime-env 

bedgraph=$1
describer=$(echo ${bedgraph} | sed -e "s/.bedgraph$//")

bedtools merge -c 4,4,4 -o count,mean,collapse -delim "," -i /project2/gilad/briana/threeprimeseq/data/bedgraph/$1 > /project2/gilad/briana/threeprimeseq/data/bedgraph/${describer}.peaks.bed

Run this first on the total bedgraph, TotalBamFiles_no0.bedgraph. The file has chromosome, start, end, number of regions, mean, and a string of the values.

This is not exaclty what I want. I need to go back and do genome cov not collapsing with bedgraph.

To evaluate this I will bring the file into R and plot some statistics about it.

#!/bin/bash

#SBATCH --job-name=Tgencov
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=Tgencov.out
#SBATCH --error=Tgencov.err
#SBATCH --partition=broadwl
#SBATCH --mem=40G
#SBATCH --mail-type=END


module load Anaconda3
source activate three-prime-env 


bedtools genomecov -ibam /project2/gilad/briana/threeprimeseq/data/macs2/TotalBamFiles.sort.bam -d > /project2/gilad/briana/threeprimeseq/data/bedgraph/TotalBamFiles.genomecov.bed

I will now remove the bases with 0 coverage.

awk '{if ($3 != 0) print}' TotalBamFiles.genomecov.bed > TotalBamFiles.genomecov.no0.bed 

awk '{print $1 "\t" $2 "\t"  $2 "\t" $3}' TotalBamFiles.genomecov.no0.bed > TotalBamFiles.genomecov.no0.fixed.bed

I will now merge the genomecov_no0 file with mergeGencov.sh

#!/bin/bash

#SBATCH --job-name=mergegc
#SBATCH --account=pi-yangili1
#SBATCH --time=8:00:00
#SBATCH --output=mergegc.out
#SBATCH --error=mergegc.err
#SBATCH --partition=broadwl
#SBATCH --mem=16G
#SBATCH --mail-type=END

module load Anaconda3
source activate three-prime-env 

gencov=$1
describer=$(echo ${gencov} | sed -e "s/.genomecov.no0.fixed.bed$//")

bedtools merge -c 4,4,4 -o count,mean,collapse -delim "," -i /project2/gilad/briana/threeprimeseq/data/bedgraph/$1 > /project2/gilad/briana/threeprimeseq/data/bedgraph/${describer}.gencovpeaks.bed

This method gives us 811,637 regions.

Evaluate regions

Bedgraph results

library(dplyr)

Attaching package: 'dplyr'
The following objects are masked from 'package:stats':

    filter, lag
The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union
library(ggplot2)
library(readr)
library(workflowr)
This is workflowr version 1.2.0
Run ?workflowr for help getting started
library(tidyr)

First I will look at the bedgraph file. This is not as imformative becuase it combined regions with the same counts.

total_bedgraph=read.table("../data/bedgraph_peaks/TotalBamFiles_no0.peaks.bed",col.names = c("chr", "start", "end", "regions", "mean", "counts"))

Plot the mean:

plot(sort(log10(total_bedgraph$mean), decreasing=T), xlab="Region", ylab="log10 of bedgraph region bin", main="Distribution of log10 region means from bedgraph")

Version Author Date
24c6663 Briana Mittleman 2018-07-03

I want to look at the distribution of how many bases are included in the regions.

Tregion_bases=total_bedgraph %>% mutate(bases=end-start) %>% select(bases)

plot(sort(log10(Tregion_bases$bases), decreasing = T), xlab="Region", ylab="log10 of region size", main="Distribution of bases in regions- log10")

Version Author Date
24c6663 Briana Mittleman 2018-07-03

Given the reads are abotu 60bp this is probably pretty good.

GenomeCov results

I am only going to look at the number of bases in region and mean coverage columns here because the file is really big.

total_gencov=read.table("../data/bedgraph_peaks/TotalBamFiles.gencovpeaks_noregstring.bed",col.names = c("chr", "start", "end", "regions", "mean"))

Plot the mean:

plot(sort(log10(total_gencov$mean), decreasing=T), xlab="Region", ylab="log10 of mean bin count", main="Distribution of log10 region means")

Version Author Date
24c6663 Briana Mittleman 2018-07-03
plot(sort(log10(total_gencov$regions), decreasing = T), xlab="Region", ylab="log10 of region size", main="Distribution of bases in regions- log10")

Version Author Date
24c6663 Briana Mittleman 2018-07-03

Plot number of bases against the mean:

ggplot(total_gencov, aes(y=log10(regions), x=log10(mean))) +
         geom_point(na.rm = TRUE, size = 0.1) +
         geom_density2d(na.rm = TRUE, size = 1, colour = 'red') +
         ylab('Log10 Region size') +
         xlab('Log10 Mean region coverage') + 
        ggtitle("Region size vs Region Coverage: Combined Total Libraries")

Version Author Date
24c6663 Briana Mittleman 2018-07-03

Troubleshooting

Account for split reads

In the previous analysis I did not account for split reads in the genome coveragre step. This may explain some of the long regions that are an effect of splicing. This script is

#!/bin/bash

#SBATCH --job-name=Tgencovsplit
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=Tgencovsplit.out
#SBATCH --error=Tgencovaplit.err
#SBATCH --partition=broadwl
#SBATCH --mem=40G
#SBATCH --mail-type=END


module load Anaconda3
source activate three-prime-env 


bedtools genomecov -ibam /project2/gilad/briana/threeprimeseq/data/macs2/TotalBamFiles.sort.bam -d -split > /project2/gilad/briana/threeprimeseq/data/bedgraph/TotalBamFiles.split.genomecov.bed

Now I need to remove the 0s and merge.

awk '{if ($3 != 0) print}' TotalBamFiles.split.genomecov.bed > TotalBamFiles.split.genomecov.no0.bed

awk '{print $1 "\t" $2 "\t"  $2 "\t" $3}' TotalBamFiles.split.genomecov.no0.bed > TotalBamFiles.split.genomecov.no0.fixed.bed

Use this file to run mergeGencov.sh.

total_gencov_split=read.table("../data/bedgraph_peaks/TotalBamFiles.split.gencovpeaks.noregstring.bed",col.names = c("chr", "start", "end", "regions", "mean"))

Plot the region size. I expect some of the long regions are gone.

plot(sort(log10(total_gencov_split$regions), decreasing = T), xlab="Region", ylab="log10 of region size", main="Distribution of bases in regions- log10 SPLIT")

Version Author Date
2d67ec5 Briana Mittleman 2018-07-05

Plot the region size against the mean:

Plot number of bases against the mean:

splitplot=ggplot(total_gencov_split, aes(y=log10(regions), x=log10(mean))) +
         geom_point(na.rm = TRUE, size = 0.1) +
         geom_density2d(na.rm = TRUE, size = 1, colour = 'red') +
         ylab('Log10 Region size') +
         xlab('Log10 Mean region coverage') + 
     scale_y_continuous(limits = c(0, 3)) +
        ggtitle("Combined Total Libraries SPLIT")

Investigate long regions

Some of the regions are long and probably represent 2 or more sites. This is evident in highly expressed genes such as actB. I will look at some of the long regions and make histograms with the strings of coverage in the region.

First I am going to look at chr11:65266512-65268654, this is peak 580475 I will go into the otalBamFiles.split.gencovpeaks.bed file and use:

 grep -n 65266512 TotalBamFiles.split.gencovpeaks.bed | awk '{print $6}' > loc_ch11_65266512_65268654.txt
loc_ch11_65266512_65268654=read.csv("../data/bedgraph_peaks/loc_ch11_65266512_65268654.txt", header=F) %>% t


loc_ch11_65266512_65268654_df= as.data.frame(loc_ch11_65266512_65268654)

loc_ch11_65266512_65268654_df$loc= seq(1:nrow(loc_ch11_65266512_65268654_df))
colnames(loc_ch11_65266512_65268654_df)= c("count", "loc")

ggplot(loc_ch11_65266512_65268654_df, aes(x=loc, y=count)) + geom_line() + labs(y="Read Count", x="Peak Location", title="Example of long region called as 1 peak \n ch11 65266512-65268654")

Version Author Date
9de3677 Briana Mittleman 2018-07-05

Try one more. Example. line 816811, chr:17- 79476983- 79477761

 grep -n 79476983 TotalBamFiles.split.gencovpeaks.bed | awk '{print $6}' > loc_ch17_79476983_79477761.txt
loc_ch17_79476983_79477761=read.csv("../data/bedgraph_peaks/loc_ch17_79476983_79477761.txt", header=F) %>% t

loc_ch17_79476983_79477761_df= as.data.frame(loc_ch17_79476983_79477761)

loc_ch17_79476983_79477761_df$loc= seq(1:nrow(loc_ch17_79476983_79477761_df))
colnames(loc_ch17_79476983_79477761_df)= c("count", "loc")

ggplot(loc_ch17_79476983_79477761_df, aes(x=loc, y=count)) + geom_line() + labs(y="Read Count", x="Peak Location", title="Example of long region called as 1 peak \n ch17 79476983:79477761")

Version Author Date
9de3677 Briana Mittleman 2018-07-05

This one is not multiple peaks but it does need to be trimmed.

Compare to adhoc method by Yang

Yang created an adhoc method to do this.

def main(inFile, outFile, ctarget):
    fout = open(outFile,'w')
    mincount = 10
    ov = 20
    current_peak = []
    
    currentChrom = None
    
    for ln in open(inFile):
        chrom, pos, count = ln.split()
        if chrom != ctarget: continue
        count = float(count)
        if currentChrom == None:
            currentChrom = chrom
            
        if count == 0 or currentChrom != chrom:
            if len(current_peak) > 0:
                M = max([x[1] for x in current_peak])
                if M > mincount:
                    all_peaks = refine_peak(current_peak, M, M*0.1,M*0.05)
                    #refined_peaks = [(x[0][0],x[-1][0], np.mean([y[1] for y in x])) for x in all_peaks]  
                    rpeaks = [(int(x[0][0])-ov,int(x[-1][0])+ov, np.mean([y[1] for y in x])) for x in all_peaks]
                    if len(rpeaks) > 1:
                        for clu in cluster_intervals(rpeaks)[0]:
                            M = max([x[2] for x in clu])
                            merging = []
                            for x in clu:
                                if x[2] > M *0.5:
                                    #print x, M
                                    merging.append(x)
                            c, s,e,mean =  chrom, min([x[0] for x in merging])+ov, max([x[1] for x in merging])-ov, np.mean([x[2] for x in merging])
                            #print c,s,e,mean
                            fout.write("chr%s\t%d\t%d\t%d\t+\t.\n"%(c,s,e,mean))
                            fout.flush()
                    elif len(rpeaks) == 1:
                        s,e,mean = rpeaks[0]
                        fout.write("chr%s\t%d\t%d\t%f\t+\t.\n"%(chrom,s+ov,e-ov,mean))
                        print ("chr%s"%chrom+"\t%d\t%d\t%f\t+\t.\n"%rpeaks[0])
                    #print refined_peaks
            current_peak = []
        else:
            current_peak.append((pos,count))
        currentChrom = chrom
def refine_peak(current_peak, M, thresh, noise, minpeaksize=30):
    
    cpeak = []
    opeak = []
    allcpeaks = []
    allopeaks = []
    for pos, count in current_peak:
        if count > thresh:
            cpeak.append((pos,count))
            opeak = []
            continue
        elif count > noise: 
            opeak.append((pos,count))
        else:
            if len(opeak) > minpeaksize:
                allopeaks.append(opeak) 
            opeak = []
        if len(cpeak) > minpeaksize:
            allcpeaks.append(cpeak)
            cpeak = []
        
    if len(cpeak) > minpeaksize:
        allcpeaks.append(cpeak)
    if len(opeak) > minpeaksize:
        allopeaks.append(opeak)
    allpeaks = allcpeaks
    for opeak in allopeaks:
        M = max([x[1] for x in opeak])
        allpeaks += refine_peak(opeak, M, M*0.3, noise)
    #print [(x[0],x[-1]) for x in allcpeaks], [(x[0],x[-1]) for x in allopeaks], [(x[0],x[-1]) for x in allpeaks]
    #print '---\n'
    return allpeaks
if __name__ == "__main__":
    import numpy as np
    from misc_helper import *
    import sys
    chrom = sys.argv[1]
    inFile = "/project2/yangili1/threeprimeseq/gencov/TotalBamFiles.split.genomecov.bed"
    outFile = "APApeaks_chr%s.bed"%chrom
    main(inFile, outFile, chrom)

This is done by chromosome and takes in the TotalBam Split genome coverage file I made.I am going to look at the stats for these peaks.

YL_peaks=read.table("../data/bedgraph_peaks/APApeaks.bed", col.names = c("chr", "start", "end", "count", "strand", "score")) %>% mutate(length=end-start)

Plot the lengths

plot(sort(log10(YL_peaks$length), decreasing = T), xlab="Region", ylab="log10 of region size", main="Distribution of bases in YL regions- log10 ")

Version Author Date
a0541e3 Briana Mittleman 2018-07-06

Plot number of bases against the mean:

YLplot=ggplot(YL_peaks, aes(y=log10(length), x=log10(count))) +
         geom_point(na.rm = TRUE, size = 0.1) +
         geom_density2d(na.rm = TRUE, size = 1, colour = 'red') +
         ylab('Log10 Region size') +
         xlab('Log10 Mean region coverage') + 
        scale_y_continuous(limits = c(0, 3)) + 
        ggtitle("YL Peaks Combined Total Libraries")
library(cowplot)

Attaching package: 'cowplot'
The following object is masked from 'package:ggplot2':

    ggsave
plot_grid(splitplot, YLplot)

Version Author Date
f4f1918 Briana Mittleman 2018-07-06
a0541e3 Briana Mittleman 2018-07-06

Run this on the Nuclear Fraction Bam

#!/bin/bash

#SBATCH --job-name=Ngencov_s
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=Ngencov_s.out
#SBATCH --error=Ngencov_s.err
#SBATCH --partition=broadwl
#SBATCH --mem=40G
#SBATCH --mail-type=END


module load Anaconda3
source activate three-prime-env 

samtools sort -o /project2/gilad/briana/threeprimeseq/data/macs2/NuclearBamFiles.sort.bam /project2/gilad/briana/threeprimeseq/data/macs2/NuclearBamFiles.bam 


bedtools genomecov -ibam /project2/gilad/briana/threeprimeseq/data/macs2/NuclearBamFiles.sort.bam -d -split > /project2/gilad/briana/threeprimeseq/data/bedgraph/NuclearBamFiles.split.genomecov.bed

I modified Yang’s script to take the nuclear gencov and put the output in the data/peaks directory. I will create a wrapper to call this on chromosomes 1-22.

#!/bin/bash

#SBATCH --job-name=w_getpeakYL
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=w_getpeakYL.out
#SBATCH --error=w_getpeakYL.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END

module load Anaconda3
source activate three-prime-env


for i in $(seq 1 22); do 
  sbatch callPeaksYL_Nuc.py $i
done

I can now concatenate all of these into one file:

cat * | sort -k 1,1 -k2,2n > APApeaks_nuclear_all.bed 

Thoughts:

  • Remove peaks outside 1kb of the genes

  • Remove peaks with low expression


sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] cowplot_0.9.3   bindrcpp_0.2.2  tidyr_0.8.1     workflowr_1.2.0
[5] readr_1.1.1     ggplot2_3.0.0   dplyr_0.7.6    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.19     pillar_1.3.0     compiler_3.5.1   git2r_0.24.0    
 [5] plyr_1.8.4       bindr_0.1.1      tools_3.5.1      digest_0.6.17   
 [9] jsonlite_1.6     lattice_0.20-35  evaluate_0.13    tibble_1.4.2    
[13] gtable_0.2.0     pkgconfig_2.0.2  rlang_0.2.2      Matrix_1.2-14   
[17] yaml_2.2.0       withr_2.1.2      stringr_1.4.0    knitr_1.20      
[21] fs_1.2.6         hms_0.4.2        rprojroot_1.3-2  grid_3.5.1      
[25] tidyselect_0.2.4 reticulate_1.10  glue_1.3.0       R6_2.3.0        
[29] rmarkdown_1.11   purrr_0.2.5      magrittr_1.5     whisker_0.3-2   
[33] backports_1.1.2  scales_1.0.0     htmltools_0.3.6  MASS_7.3-50     
[37] assertthat_0.2.0 colorspace_1.3-2 labeling_0.3     stringi_1.2.4   
[41] lazyeval_0.2.1   munsell_0.5.0    crayon_1.3.4