User: ajsn6c

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ajsn6c0
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Posts by ajsn6c

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Comment: C: How Can I Convert Bam/Sam To Wiggle
... This works great! What are the output values though for say ChIP-seq data thats been trimmed, bowtie2 aligned, duplicates removed and indexed? I know that the first column is the position, but do 5,7,12,and 15 represent raw read counts or rpkm values? Thanks! 10030 5 10040 7 10050 12 10060 15 ...
written 19 months ago by ajsn6c0
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Answer: A: Enhancers in Introns
... We use H3K4me1 and H3K27ac overlaps as putative enhancer marks. You can use Bedtools IntersectBed to overlap the two. You can download the histone peaks from UCSC Genome Browser, then use HOMER annotation to annotate the peaks and filter for introns. ...
written 19 months ago by ajsn6c0
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Comment: A: cummeRbund, extracting chr8 for scatterplot
... You know what, its really a scaling size issue. For one sample I have a fpkm value of 80,000 and the other sample only goes up to about 5,000 fpkm. So cummeRbund creates a log transformed scale for the axis with 80,000 fpkm, but not the other one. Im trying to delete the few points where they are ab ...
written 23 months ago by ajsn6c0
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Comment: A: cummeRbund, extracting chr8 for scatterplot
... library(cummeRbund) #load cummeRbund packages cuff_data <- readCufflinks('Wt_vs_Control_Blind_Dispersion_chr8') #reads diff_out file from cuffdiff pdf(file="practice.pdf") #name of scatter plot csScatter(genes(cuff_data), 'S1', 'S2') #creates scatter plot of all gene fp ...
written 23 months ago by ajsn6c0

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