User: sikhtechai

gravatar for sikhtechai
sikhtechai30
Reputation:
30
Status:
New User
Location:
Last seen:
2 days, 11 hours ago
Joined:
3 years, 3 months ago
Email:
s**********@gmail.com

Posts by sikhtechai

<prev • 17 results • page 1 of 2 • next >
0
votes
1
answer
1.9k
views
1
answers
Comment: C: Correlating ChIP-Seq peaks with isoform level expression
... May I know how you generated the gene list with those three categories? I have having similar dataset and want to perform this similar analysis. Thanks in advance! ...
written 3 days ago by sikhtechai30
0
votes
1
answer
60
views
1
answers
Comment: C: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
... That's a very good advice! Thank you very much for your suggestion! ...
written 3 days ago by sikhtechai30
0
votes
0
answers
43
views
0
answers
Defining bivalent promoters with H3K4me3 and H3K27me3 ChIPseq data
... Dear all, Imagine, you have H3K4me3 and H3K27me3 ChIPseq data. How would you befine bivalent promoters? Like, could you please explain possible workflow? Like, for example, after peak calling, would you use bedtools to intersect and find the overlapping regions with both those marks? Or something e ...
chip-seq written 3 days ago by sikhtechai30
0
votes
1
answer
60
views
1
answers
Comment: C: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
... Thank you very much for your quick answer! It makes sense. However, regarding answer 3, the control file here means, the sample which did not receive the drugs. It is not like, the input control or IgG control for ChIP. Then do you think I should still include them for learning the model? Or, learn ...
written 3 days ago by sikhtechai30
3
votes
1
answer
60
views
1
answer
Questions related to ChromHMM+using MACS2 peak calling output bed file as input for ChromHMM?
... Hi all! I have 3 questions about running the ChromHMM tool to find the combinatorial states of multiple ChIPseq data. 1. I have replicate ChIPseq data(4 replicates each) for H3K4me3 and H3K27me3 in control vs treatment. For ChromHMM, do I need to merge all the replicates and then run it, or I can ...
chip-seq macs2 chromhmm written 3 days ago by sikhtechai30 • updated 3 days ago by Ar860
0
votes
0
answers
89
views
0
answers
Accurately identifying long non coding RNA from stranded total RNAseq(rRNA depleted)
... I have stranded Total RNaseq sequencing data(rRNA depleted) between two condition. Apart from gene level RNAseq analysis to find differential expression of genes, I am interested to look for non-coding RNA captured by total RNAseq. What could be the strategy for accurately mapping and quantifying fo ...
alignment rna-seq sequencing written 7 weeks ago by sikhtechai30
0
votes
2
answers
275
views
2
answers
Problem with demultiplexing illumina dual indexed libraries
... Hello, I am currently facing a problem regarding demultiplexing my dual indexed reads run on Hiseq 2000. Basically, the Lane summary looks like this: ![Whole flow cell summary][1] So, each lane, having around 230 million reads. Sequencing went fine. I have put 3 samples per lane, to have around 70 ...
illumina next-gen sequence rna-seq sequencing written 10 weeks ago by sikhtechai30 • updated 10 weeks ago by Gabriel R.2.6k
0
votes
0
answers
826
views
0
answers
Comment: C: How to rescale aggregation plots of different ChIP-seq datasets using ngsplot?
... Hi, I have the same issue! Did you find any solution? ...
written 5 months ago by sikhtechai30
0
votes
0
answers
584
views
0
answers
Comment: C: Normalizing ChIP-seq Data To Spike-In Control
... Did you find a way to solve this problem? I am having the exact same issue! ...
written 5 months ago by sikhtechai30
0
votes
3
answers
2.3k
views
3
answers
Comment: C: How to find out whether Chip-seq peaks falls within promoter or enhancer region
... @geek_y: Hi! Thanks for your answer! It is really helpful! So, after I do the intersection of my Peak file with the Enhancer file, how can I do enrichment analysis? I mean, the intersection will give me the genomic regions, which are enhancer, but how to associate them with genes? Many thanks for ...
written 5 months ago by sikhtechai30

Latest awards to sikhtechai

Popular Question 6 weeks ago, created a question with more than 1,000 views. For mm10 enhancer annotation for ngs.plot.r
Popular Question 9 months ago, created a question with more than 1,000 views. For mm10 enhancer annotation for ngs.plot.r

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 540 users visited in the last hour