User: srhic

gravatar for srhic
srhic0
Reputation:
0
Status:
New User
Last seen:
1 week, 6 days ago
Joined:
10 months, 1 week ago
Email:
s*****@nyu.edu

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by srhic

<prev • 26 results • page 1 of 3 • next >
0
votes
1
answer
119
views
1
answers
Comment: C: Chip-Seq input normalization with deeptools
... You are correct. I input normalized my samples, filtered out negative values and the resulting plots looked pretty much identical to what I had without input normalization. However, I am still concerned about about the input being higher than IP. I am sure some of these would be blacklisted areas ...
written 13 days ago by srhic0
0
votes
1
answer
119
views
1
answers
Comment: C: Chip-Seq input normalization with deeptools
... Thanks, I will check it out ...
written 13 days ago by srhic0
2
votes
1
answer
119
views
1
answer
Chip-Seq input normalization with deeptools
... Hello, I want to visualize the difference in chip-signal at specific locations by making average profiles using deeptools. For this I have generated RPKM normalized bigwig files for my treatment and control conditions and plotting them gives me good results. However, these files are not input norm ...
deeptools chip-seq written 14 days ago by srhic0 • updated 13 days ago by jared.andrews075.2k
0
votes
2
answers
101
views
2
answers
Comment: C: Removing outliers from bigwig files
... I tried this and it worked perfectly. However, one confusion I have is if I should normalize the bigwig files for each condition separately. For example, if I have one control and multiple treatment conditions, should I use the 99 percentile of each treatment to scale down its outliers or scale dow ...
written 4 weeks ago by srhic0
0
votes
2
answers
101
views
2
answers
Comment: C: Removing outliers from bigwig files
... Thanks! I will try this ...
written 4 weeks ago by srhic0
0
votes
2
answers
101
views
2
answers
Comment: A: Removing outliers from bigwig files
... Thanks for the replies. I have already removed pcr duplicates from the bam files but I still get outliers in some areas in both control and treatment samples. These spikes are up to 20 or 30 times higher than the average coverage in most areas. I think I will try removing the top 1 percentile in R. ...
written 4 weeks ago by srhic0
0
votes
2
answers
101
views
2
answers
Removing outliers from bigwig files
... Hello, I have some atac-seq and chip-seq data which I have processed using deeptools to generate normalized bigwig files. I am now using these bigwig file to plot profiles over regions of interest but am having problems with outliers distorting the plots in certain regions. I was wondering if there ...
deeptools next-gen chip-seq written 4 weeks ago by srhic0
0
votes
1
answer
113
views
1
answer
Question about interpreting PCA values in HiC data
... Hello, I have a question about PCA analysis specifically as it relates to HiC data. A common approach in HiC analysis is perform a PCA analysis on interaction matrices and classify genomic regions as active or repressed (A & B compartments) based on their Principal component 1 value. Any region ...
compartments pca hic written 8 weeks ago by srhic0
0
votes
0
answers
179
views
0
answers
Comment: C: HOMER HiC interactions
... Thanks, I found this paper which shows that the number of interactions detected by HOMER is directly related to the number of reads in a sample. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493985/ I assume this is why I am getting more interactions in merged samples but I am still unsure what w ...
written 4 months ago by srhic0
0
votes
0
answers
179
views
0
answers
Comment: C: HOMER HiC interactions
... They dont seem to be duplicates though it is hard to check that systematically. ...
written 4 months ago by srhic0

Latest awards to srhic

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1764 users visited in the last hour