User: c.chakraborty

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c.chakraborty140
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Posts by c.chakraborty

<prev • 35 results • page 1 of 4 • next >
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Answer: A: Meaningful DE using rpkm values in a RNA-Seq analysis
... Use raw read counts for genes and put them in DESeq2 or EdgeR for analysis. With RPKM, your expression is normalized to the length of the transcript. Thus if you have a very long transcript, the normalized value will be lower. As it is a practice in RPKM based analysis, to use a cutoff for expressio ...
written 4 weeks ago by c.chakraborty140
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Comment: C: How to get the position of a transcript on chromosome with ncbi refseq_ncrna id?
... Did you choose Refseq ncRNA ID from the dropbox menu? ...
written 10 weeks ago by c.chakraborty140
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Answer: A: How to get the position of a transcript on chromosome with ncbi refseq_ncrna id?
... Use BioMart from ENSEMBL. 1. Go to the ENSEMBL BioMART tool. 2.Choose database- usually I choose ENSEMBL genes 3.On the right hand, you will find Filters, click on it and then choose genes. 4. In the second drop down you will find - Input External references. Tick this one. On the left, there is a ...
written 10 weeks ago by c.chakraborty140
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Comment: C: RNA Seq analysis of rice samples
... Have you run a PCA analysis with your data from the samples? It can tell you if the control and the treated samples are distinct enough for further differential gene expression analysis. Alternatively, you can try running STAR or hisat2 alignment followed by DESEq2 analysis. Cufflinks normalizes th ...
written 5 months ago by c.chakraborty140
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Comment: C: RNA Seq analysis of rice samples
... Are you sure its fpkm < 0? Could you put a screenshot of the cufflinks file? ...
written 5 months ago by c.chakraborty140
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Answer: A: Extract Ensembl IDs column using a data file
... Use bioMart from bioconductor, to extract the ENSEMBL IDs of your genes.https://www.bioconductor.org/packages/devel/bioc/vignettes/biomaRt/inst/doc/biomaRt.html ...
written 5 months ago by c.chakraborty140
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list to one fasta file
... Dear all, I used biomaRt to retrieve the 3'UTR sequences of 1527 transcpts, using their refseq ids: for (i in uniquetrans[,1]) { sequences[i] = getSequence(id = i,type = "refseq_mrna",seqtype = "3utr", mart = ensembl, verbose = FALSE) } The sequences were retrieved, but now, I ha ...
fasta R biomar written 6 months ago by c.chakraborty140 • updated 5 months ago by RamRS24k
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Answer: A: Where Can I find protein-protein interactions data ?
... Try STRING db for networks ...
written 10 months ago by c.chakraborty140
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Answer: A: Panther pathway gene list counts
... I am not sure if this helps or not, but since the GOIDs are from GO consortium, maybe you can search for the GO term of your interest say- GO:0043066, and then this navigates you to the page with links to gene and gene products, ontology etc. And from there you can select gene and gene products and ...
written 10 months ago by c.chakraborty140
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Answer: A: gene expression analysis using RNA seq data
... Hey I am adding these links so you can go through to understand the normalization of FPKM/RPKM and TPM- https://statquest.org/2015/07/09/rpkm-fpkm-and-tpm-clearly-explained/ https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/ FPKM of a gene (say ABB) is ...
written 12 months ago by c.chakraborty140

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