User: emilyprice16

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emilyprice1620
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Posts by emilyprice16

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Comment: C: DiffBind consensus peak set query
... Thank you so much Rory, that is really helpful! ...
written 4 weeks ago by emilyprice1620
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DiffBind consensus peak set query
... I know that in making a consensus peakset you can set a threshold of how many samples the peak has to occur in. However I want to know if you can also set this by group. Say I have 3 groups A, B and C and 4 samples in each. Instead of setting the threshold to occur in say 4 out of 12 samples can I s ...
diffbind written 4 weeks ago by emilyprice1620 • updated 4 weeks ago by Rory Stark920
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Comment: C: MultiBamSummary for correlating ChIPseq datasets
... Thank you. I will definitely have a play around with the bin size. I noticed in a separate post you commented that it is probably better to use multibigwigsummary as I can first normalise to input. So I think I will continue that way! ...
written 4 months ago by emilyprice1620
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Comment: C: Plotting ChIP seq signals in specific regions
... Just had a look into that and seems perfect what I want. Thank you for your help! ...
written 4 months ago by emilyprice1620
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MultiBamSummary for correlating ChIPseq datasets
... I want to be able to determine if the enrichment of a specific histone modification is correlated with the enrichment in a specific TF binding in genomic regions that these both overlap. Having looked through examples I see you can use multiBamSummary and plotCorrelation to see if you have correlati ...
chip-seq multibamsummary written 4 months ago by emilyprice1620 • updated 4 months ago by Rory Stark920
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Comment: C: Plotting ChIP seq signals in specific regions
... Reading that back it is quite confusing, sorry! But I managed to solve what I wanted to do, I just misunderstood part of the way computeMatrix works. However my only issue now is I have 4 replicates for each TF, therefore for each TF I have 4 bigwig files. Is there any way to merge these so I can ha ...
written 4 months ago by emilyprice1620
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Comment: C: Using bedtools to identify genes that have overlapping chip-seq peaks
... You can use the bedtools intersect function to find those peaks that overlap between multiple bed files. You can then use the closest function in bedtools to annotate the nearest gene to those peaks. ...
written 4 months ago by emilyprice1620
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Answer: A: genome coordinates hg19 from UCSC genome browser
... You can find them here: https://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes ...
written 4 months ago by emilyprice1620
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Comment: C: Plotting ChIP seq signals in specific regions
... Thank you this is really helpful. I’ve been able to follow the documentation and done some plots. I do have another question though for each TF I have a separate bigwig file. So far I have put both TF bed files for -R and the two corresponding bigwig files for -S with a space in between. However whe ...
written 4 months ago by emilyprice1620
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Plotting ChIP seq signals in specific regions
... I was wondering if anyone can help me. Looking on IGV at my ChIP seq data I am noticing that there seems to be an overlap between 2 different TFs binding to the same location. I know you can do read density plots to show the location across the gene where there is the highest read density. Is there ...
chip-seq written 4 months ago by emilyprice1620

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