User: bharata1803

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bharata180340
Reputation:
40
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New User
Location:
Japan
Last seen:
3 months, 3 weeks ago
Joined:
3 years, 10 months ago
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b**********@gmail.com

Posts by bharata1803

<prev • 55 results • page 1 of 6 • next >
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Comment: C: Inconsistent result between limma/voom and DESeq2
... but still, I am confused by why DESeq2 and limma voom method report it differently ...
written 3 months ago by bharata180340
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Comment: C: Inconsistent result between limma/voom and DESeq2
... If I used one of the library incorrectly, I don't think I will get most result consistently. As you can see from the first picture, most result from DESeq2 and limma voom method are consistent (logFC sign are the same) and only small number of genes are problematic. That's why I think I don't need t ...
written 3 months ago by bharata180340
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Inconsistent result between limma/voom and DESeq2
... So, I am trying to find DE genes in a cancer-normal dataset. I am using both DESeq2 and limma/voom method. Interestingly, I found many genes that are significance (adj p value <0.05) but the log2FoldChange sign is on the opposite. So, for example, in DESeq2 it is reported as down regulated but in ...
rnaseq limma deseq2 voom limma-voom written 3 months ago by bharata180340 • updated 3 months ago by Gordon Smyth36k
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CAGEr get TSS in bed file
... Hello,  I am trying CAGEr library for FANTOM5 data. The current FANTOM5 CTSS is mapped/aligned to hg19. So, I want to learn hw to generate CTSS dta by realigned it to HG38. My workflow is: 1. Get fastq from FANTOM5 bam 2. ALigned bam to HG38 reference genome 3. Using CAGEr to get CTSS data   I ...
cager promoter cage tss written 3 months ago by bharata180340
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Comment: C: DESeq2 with several biological replicates
... hello, it seems it is not biological replicates but technical replicates. the biological sample is the same. it just run/sequenced 5 times. Can you give some suggestion? If not, I will just take 1 sample from every patient to make things simpler. If it is from the same sample and just sequence 5 tim ...
written 4 months ago by bharata180340
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Comment: C: DESeq2 with several biological replicates
... Actually it is a public data. So, I am not so sure myself. This is the link: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP069212 From the paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5316832/ they only mentioned like this: Total RNA from 60 samples from 20 Chinese HCC patients was sequ ...
written 4 months ago by bharata180340
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Comment: C: DESeq2 with several biological replicates
... The number of patients is 20. Each patients has 5 normal rna-seq reads and 5 tumor rna-seq reads (matched). ...
written 4 months ago by bharata180340
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DESeq2 with several biological replicates
... Hello, Is there any guide or tutorial to process RNA-seq sample with biological replicates? I have 2 conditions, normal and tumor. The total number of sample is 20 with each normaland tumor has 5 biological replicates. Thanks. ...
rnaseq deseq2 differential gene expression written 4 months ago by bharata180340
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WGCNA package : identification of hub genes
... I have a research problem that I want to solve. Basically, I want to find important genes per module that is generated from WGCNA algorithm. I define important genes as hub genes. Hub genes is defined as genes that have most connectivity. I read from some paper that basically the calculation is to ...
wgcna written 14 months ago by bharata180340
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Comment: C: DESeq2 result really different when only use some sample vs all sample
... The reason I subset my sample is the DESeq2 log fold change is really weird. There are not many genes that are differentially expressed and only around ~600 genes with p-value adjusted less than 0.05 (~500 genes have logfoldchange >0.65 or <-0.65, |0.65| is my cut for up/down regulated). So, I ...
written 16 months ago by bharata180340

Latest awards to bharata1803

Popular Question 2.0 years ago, created a question with more than 1,000 views. For Limma log transform RNA-seq and microarray
Popular Question 2.0 years ago, created a question with more than 1,000 views. For DESeq2 with multiple conditions
Popular Question 2.0 years ago, created a question with more than 1,000 views. For DESeq2 Error NA values
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Calculate DESeq2 fold change of 1 gene to 1 of the sample
Popular Question 2.0 years ago, created a question with more than 1,000 views. For DESeq2 Error NA values
Popular Question 2.8 years ago, created a question with more than 1,000 views. For DESeq2 rlog function takes too long

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