User: bioinfo

gravatar for bioinfo
bioinfo0
Reputation:
0
Status:
New User
Location:
Last seen:
23 hours ago
Joined:
1 year, 7 months ago
Email:
t********@gmail.com

Posts by bioinfo

<prev • 11 results • page 1 of 2 • next >
0
votes
1
answer
31
views
1
answer
Double nested design in DESeq2
... Hi, I am analyzing RNA-seq data with four factors: Condition (WT and MT), CellLine (2 cell lines in each condition), Replicate (3 replicates in each cell line) and library (paired pull-down and control for a replicate): total 2*2*3*2=24 samples (Table is the below). I would like to find the differen ...
deseq2 written 1 day ago by bioinfo0 • updated 17 hours ago by Michael Love20k
1
vote
1
answer
85
views
1
answer
DESeq2 for ChIP-seq
... I have ChIP-seq datasets as the following:     Cell Type Condtion 1 A Input WT 2 A Pulldown WT 3 B Input WT 4 B Pulldown WT 5 C Input MT 6 C Pulldown MT 7 D ...
diffbind deseq2 written 3 months ago by bioinfo0 • updated 3 months ago by Michael Love20k
0
votes
2
answers
162
views
2
answers
Comment: C: DESeq2: possible to compare read counts at single nucleotide level ?
... By the way, when ChIP-seq data is analyzed by DESeq2 for differential binding (for example: diffBind), the region is pre-defined by peak calling software such as MACS. Here, the size of region is variable. If read depth is not good for DESeq2, do you think that small size of region is also not good ...
written 4 months ago by bioinfo0
0
votes
2
answers
162
views
2
answers
Comment: C: DESeq2: possible to compare read counts at single nucleotide level ?
... Thanks for your help !! ...
written 4 months ago by bioinfo0
0
votes
2
answers
167
views
2
answers
Comment: C: Differential ChIP-seq analysis
... Thanks for your answer ! ...
written 4 months ago by bioinfo0
0
votes
2
answers
167
views
2
answers
Comment: C: Differential ChIP-seq analysis
... Thanks for your answer. It is much clearer now to me. By the way, in the website you mentioned, I cannot read math notation in the wrapping up remarks probably due to browser formatting. Can you check it? ...
written 4 months ago by bioinfo0
2
votes
2
answers
167
views
2
answers
Differential ChIP-seq analysis
... I would like to compare two conditions with each two ChIP-seq (H3K27me3) samples. I searched for tools for differential binding and found that many including diffbind and csaw compares two conditions with read counts from pull down library only, not using input/control library/read count. The csaw h ...
diffbind csaw written 4 months ago by bioinfo0 • updated 4 months ago by Rory Stark2.6k
3
votes
2
answers
162
views
2
answers
DESeq2: possible to compare read counts at single nucleotide level ?
... Hi, I have some candidate genomic regions of interest and would like to see if they are differentially expressed between two conditions. Each condition has three biological replicates. Because I cannot define the boundaries of the candidate genomic regions exactly (they are not annotated with gene ...
rnaseq deseq2 written 4 months ago by bioinfo0 • updated 4 months ago by Gordon Smyth35k
0
votes
1
answers
164
views
1
answers
Comment: C: Few significance in DESeq2
... Thanks for your help. I agree with you. I don't want to do post-processing the p-values to have significance. I can conclude that they do not have significant genes. But it is still unclear that why the distribution of p-value is not flat in the case of no significant gene. If I understand you corre ...
written 6 months ago by bioinfo0
0
votes
1
answers
164
views
1
answers
Comment: C: Few significance in DESeq2
... Hi Michael, Thanks for your answer. You are right. In PCA plot, the samples are intermingled regardless of conditions. I understand that there are few significant genes in this case. However, while I expect that the distribution of p-value is almost flat in the case, I currently have some depletion ...
written 6 months ago by bioinfo0

Latest awards to bioinfo

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 2.2.0
Traffic: 308 users visited in the last hour