User: emilyprice16

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emilyprice1620
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Posts by emilyprice16

<prev • 13 results • page 1 of 2 • next >
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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 5 weeks 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 5 weeks 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 5 weeks ago by emilyprice1620 • updated 5 weeks ago by Rory Stark880
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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 5 weeks 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 5 weeks 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 5 weeks 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 5 weeks 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 5 weeks ago by emilyprice1620
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Comment: C: Bedtools fisher test error
... Thank you! When I used sed to remove crlf and then performed the fisher test it worked! ...
written 6 weeks ago by emilyprice1620
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Bedtools fisher test error
... I want to run the bedtools fisher command. For this I first sort my files using `sort -k1,1 -k2,2n`. When I go to run the fisher test: bedtools fisher -a a_sorted.txt -b b_sorted.txt -g rn6_chrom_sorted.txt It says exiting integer conversion of a string “282763074 What am I doing wrong ...
bedtools fisher written 6 weeks ago by emilyprice1620 • updated 6 weeks ago by _r_am31k

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