User: emilyprice16
emilyprice16 • 20
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Posts by emilyprice16
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... 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
emilyprice16 • 20
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... Just had a look into that and seems perfect what I want. Thank you for your help! ...
written 5 weeks ago by
emilyprice16 • 20
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... 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 ...
written 5 weeks ago by
emilyprice16 • 20
• updated
5 weeks ago by
Rory Stark • 880
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... 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
emilyprice16 • 20
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... 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
emilyprice16 • 20
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... You can find them here:
https://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes ...
written 5 weeks ago by
emilyprice16 • 20
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... 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
emilyprice16 • 20
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... 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 ...
written 5 weeks ago by
emilyprice16 • 20
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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
emilyprice16 • 20
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... 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 ...
written 6 weeks ago by
emilyprice16 • 20
• updated
6 weeks ago by
_r_am ♦ 31k
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