User: emilyprice16
emilyprice16 • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- Last seen:
- 4 weeks, 1 day ago
- Joined:
- 9 months, 3 weeks ago
- Email:
- e***********@me.com
Posts by emilyprice16
<prev
• 15 results •
page 1 of 2 •
next >
0
votes
1
answer
111
views
1
answers
Comment:
C: DiffBind consensus peak set query
... Thank you so much Rory, that is really helpful! ...
written 4 weeks ago by
emilyprice16 • 20
0
votes
1
answer
111
views
1
answer
... 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 ...
written 4 weeks ago by
emilyprice16 • 20
• updated
4 weeks ago by
Rory Stark • 920
0
votes
2
answers
219
views
2
answers
... 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
emilyprice16 • 20
0
votes
1
answer
252
views
1
answers
... Just had a look into that and seems perfect what I want. Thank you for your help! ...
written 4 months ago by
emilyprice16 • 20
0
votes
2
answers
219
views
2
answers
... 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 4 months ago by
emilyprice16 • 20
• updated
4 months ago by
Rory Stark • 920
0
votes
1
answer
252
views
1
answers
... 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
emilyprice16 • 20
1
vote
0
answers
287
views
0
answers
... 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
emilyprice16 • 20
1
vote
2
answers
223
views
2
answers
... You can find them here:
https://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes ...
written 4 months ago by
emilyprice16 • 20
0
votes
1
answer
252
views
1
answers
... 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
emilyprice16 • 20
1
vote
1
answer
252
views
1
answer
... 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 4 months ago by
emilyprice16 • 20
Latest awards to emilyprice16
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1565 users visited in the last hour