User: ag1805x

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ag1805x10
Reputation:
10
Status:
New User
Location:
University of Allahabad
Website:
http://ag1805x.github.io/
Twitter:
ag1805x
Last seen:
11 hours ago
Joined:
1 year, 6 months ago
Email:
a******@outlook.in

I am currently working as a Junior Research Fellow at the Centre of Bioinformatics, University of Allahabad. I hold an undergraduate (B.Sc.) degree in Biotechnology from West Bengal University of Technology, India and a postgraduate (M.Sc.) degree in Bioinformatics from Alagappa University, India. My current research interests include stem cell bioinformatics, RNA-seq data analysis and network biology.

Posts by ag1805x

<prev • 15 results • page 1 of 2 • next >
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Comment: C: tximport transcript missing
... Instead of generating the tx2gene file from GTF file or ensembldb, why not generate it from the reference transcriptome from which the index was generated. I encountered the same missing transcript problem while working with kallisto and this is a probable solution I found. https://gist.github.com ...
written 14 hours ago by ag1805x10
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Design for introducing batch effect in DESeq2
... I have RNAseq data taken from two different ENA project IDs (PrjA & PrjB). Both PrjA & PrjB contains test and control samples. PrjA was PE 50bp sequencing while PrjB was SE 100bp. Is it possible we can combine the data to identify DEG between test and control? Would batch effect removal by C ...
edger deseq2 combat rna-seq batch effect written 19 days ago by ag1805x10 • updated 19 days ago by swbarnes2310
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How to arrange multiple plots into one page in NOISeq?
... I am using NOISeq to generate Biodetection plot. I have 6 samples and need to place the plots for each sample side by side for easy comparison. As per the manual, it seems I can only visualise two at a time. Is there a way to arrange all the six plots in 2 columns and 3 rows. I tried the code: ...
noiseq rna-seq quality control written 23 days ago by ag1805x10
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Comment: C: WGCNA from different lengths RNAseq read
... Before we can apply VST in DESeq2 we have to normalize the data. Now Performing VST separately would mean normalizing data separately. Would that be good? > Success is by no means guaranteed, but it's worth a try. How do I judge success? Any parameter you would suggest. ...
written 4 months ago by ag1805x10
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WGCNA from different lengths RNAseq read
... Is it advisable to create WGCN from RNA-seq data generated on different platforms with different read lengths but processed the same way? Suppose I have 3 datasets with each containing 5 CASE and 5 CONTROL samples. ...
rnaseq network wgcna co-expression written 4 months ago by ag1805x10 • updated 4 months ago by Peter Langfelder2.2k
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Comment: C: DESeq2 FPKM normalization
... So if we need to compare between two sets of data from two different experiments, is it worth using COMBAT to remove batch effect and then use edgeR to normalize by TPM and DE analysis? ...
written 11 months ago by ag1805x10
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Comment: C: log2FoldChange calculation in DESeq2 output
... When calculating fold change how is the reference group determined? ...
written 14 months ago by ag1805x10
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Comment: C: "Over-correction" in the size-factors of the DESeq2 package
... What is a good range for size factors? In the manual I saw it should be near to 1. How much can it vary?  ...
written 14 months ago by ag1805x10
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What are the different strategies to filter out low count genes?
... What are the different strategies to filter low count genes? Some of the ones I have seen in different papers are: rowSums(count)>0 rowVariance(count)>1 ...
rnaseq deseq2 differential gene expression written 14 months ago by ag1805x10 • updated 14 months ago by Wolfgang Huber13k
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Comment: C: Too many (?) differentially expressed genes - edgeR and DESeq
... Hi Darya, I am working with something similar. Even I found about 49% of the ~20k protein Coding genes to be deferentially expressed. If you could share how you dealt with this or justified the observation. ...
written 14 months ago by ag1805x10

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