User: Susmita Mandal

Reputation:
20
Status:
New User
Location:
Bangalore
Last seen:
2 days, 3 hours ago
Joined:
4 months, 4 weeks ago
Email:
s*****************@gmail.com

Posts by Susmita Mandal

<prev • 35 results • page 1 of 4 • next >
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Genome Annotations? RepeatMasker class/family? Regulation?
... Hi everybody, I want to plot my genes of interest coinciding with the enrichment sites from another paper. But the other paper has not provided a particular table of those sites but an excel sheet giving genome annotations of regulation, repeat masker classes and family with the fold enrichment and ...
annotation ngs rna-seq repeatmasker written 3 days ago by Susmita Mandal20
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ChIP-Seq density plot of the TSS regions?
... Hello everyone, I have done ChIP-Seq analysis alllele specific way somehow, I think. I aligned the ChIP-Seq data to both the parental genomes and then I merged the aligned BAM files and I did peak calling on the merged BAM file using MACS2. I got a BED file and a bedgraph file from it. I intersect ...
bedtools deeptools ase chip-seq igv written 11 days ago by Susmita Mandal20 • updated 10 days ago by i.sudbery3.7k
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How to include genes having negative fold change in the log2 FC plot?
... Hello everyone, I am doing expression analysis on samples having different cell types and their conversions. While doing the fold change of few genes w.r.t. to one cell type, I am getting some negative values of few genes in the other cell types and thus I cannot include them in the log2 FC plot. I ...
ngs log2 ase rna-seq fold change written 20 days ago by Susmita Mandal20 • updated 20 days ago by swbarnes24.8k
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Comment: C: ChIP-Seq Analysis allele specific way?
... So far I understood that 1. Align the sample to both the parental genomes. 2. Merge the SAM/BAM file. 3. Use SNPsplit to get tags for allele specific. 4. Run the BAM file for peak calling Correct me if I'm wrong. And also how to quantify? ...
written 26 days ago by Susmita Mandal20
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Comment: C: ChIP-Seq Analysis allele specific way?
... Thank you for the response. I have few questions though. How to do SNPsplit? On both the differnet alignment files or should I merge it. and regarding calling peaks, what is the merged sample and how to quantify according to parent of origin? ...
written 26 days ago by Susmita Mandal20
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ChIP-Seq Analysis allele specific way?
... Hello everyone, I am about to do ChIP-Seq analysis allele specific way. I have not done ChiP-Seq analysis practically, but I have some idea about how to do it. The problem is I'm not getting any answers for doing ChIP Seq allele specific way. I have done allele specific RNA Seq analysis. I have the ...
vcf chip-seq ngs macs2 ase written 27 days ago by Susmita Mandal20 • updated 27 days ago by Devon Ryan88k
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Comment: C: What is RPKM/FPKM > 1 or 3 or 5?
... What would you suggest instead? ...
written 4 weeks ago by Susmita Mandal20
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Comment: C: What is RPKM/FPKM > 1 or 3 or 5?
... Does this cutoff means that all the genes in a particular sample are having at least this cut-off RPKM? ...
written 4 weeks ago by Susmita Mandal20
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Comment: C: What is RPKM/FPKM > 1 or 3 or 5?
... And how do you decide which ones are the "expressed" genes? ...
written 4 weeks ago by Susmita Mandal20
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What is RPKM/FPKM > 1 or 3 or 5?
... Hello all, I have a very basic question. In many papers and analysis we see analysis are been doing using genes having a threshold like RPKM/FPKM >1 or 3 or 5. What is this threshold? What does it mean and how do you calculate it? I'm having trouble understanding this and finding papers/articles ...
rpkm fpkm ngs rna-seq normalization written 4 weeks ago by Susmita Mandal20 • updated 4 weeks ago by johnsonnathant70

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