User: c.chakraborty

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c.chakraborty130
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Posts by c.chakraborty

<prev • 32 results • page 1 of 4 • next >
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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 8 weeks ago by c.chakraborty130
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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 8 weeks ago by c.chakraborty130
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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 11 weeks ago by c.chakraborty130
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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 3 months ago by c.chakraborty130 • updated 10 weeks ago by RamRS22k
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Answer: A: Where Can I find protein-protein interactions data ?
... Try STRING db for networks ...
written 7 months ago by c.chakraborty130
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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 7 months ago by c.chakraborty130
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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 8 months ago by c.chakraborty130
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Comment: C: Gene (mRNA) - Protein Interaction databases and prediction
... I am not really sure if there is one golden standard rule to do it. But, if I have to do this, I will find what motifs do my RBPs have and search literature for the sequences that these motifs can bind to, say a motif recognizes AU rich sequences. Then I record the sequence of that motif or motifs ...
written 10 months ago by c.chakraborty130
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Answer: A: Gene (mRNA) - Protein Interaction databases and prediction
... I found these two- http://pri.hgc.jp/ http://lulab.life.tsinghua.edu.cn/postar2/rbp2.php But, I am not sure about reliability. Usually RBPs interact mRNAs with specific domains like RRMs, zinc-fingers etc. If I know which domain my protein has, I would data-mine literature to get probable RNA bindin ...
written 10 months ago by c.chakraborty130
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Answer: C: equal distance between groups in a barplot
... Problem solved: barplot(david_go__ord_foldenr$Fold.Enrichment, names.arg = david_go__ord_foldenr$Description, horiz = TRUE, space = 0.1, cex.names = 0.5, cex.axis = 0.6, col = "blue", xlim = c(0,3)) ...
written 10 months ago by c.chakraborty130 • updated 10 months ago by zx87547.5k

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Supporter 13 months ago, voted at least 25 times.

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