User: pixie@bioinfo

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pixie@bioinfo1.3k
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Posts by pixie@bioinfo

<prev • 189 results • page 1 of 19 • next >
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Comment: C: Suggestion regarding DESeq design of experiment
... Okay thats great ..thanks ...
written 10 weeks ago by pixie@bioinfo1.3k
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Comment: C: Suggestion regarding DESeq design of experiment
... So the design is fine or should there be any other factors considered ? ...
written 10 weeks ago by pixie@bioinfo1.3k
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Suggestion regarding DESeq design of experiment
... Hello, I need some help regarding this group of RNA-seq data sets on different stress conditions (say A, B and C). The authors who actually performed these experiments performed cluster analysis using FPKM and normalized across all the stress conditions. In the paper, they mentioned **they have kept ...
rna-seq written 10 weeks ago by pixie@bioinfo1.3k • updated 10 weeks ago by grant.hovhannisyan1.4k
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Comment: C: How to make cluster from gene read count?
... you need to calculate the z-scores ((x-mean)/sigma) for the counts. From this, follow any tutorial on plotting in R. You should be able to get the above plots. With CLUST, you can get similar plots. https://github.com/BaselAbujamous/clust ...
written 3 months ago by pixie@bioinfo1.3k
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Answer: A: How to make cluster from gene read count?
... Try out CLUST https://baselabujamous.com/computational-methods/clust/ Read counts, FPKM, TPM etc are accepted in that. Regarding genes, you might want to leave out genes which show zero or low variance across samples over and above the minimum cutoff for genes. ...
written 3 months ago by pixie@bioinfo1.3k
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Comment: C: Constructing nucleotide sequence after incorporating SNPs from SIFT file
... Dear @finswimmer, Thanks so much for the pipeline. It worked smoothly. My ultimate goal is to display the reference and altered sequences gene-wise (based on user's gene query) on a browser. So in the output.fa, how will I keep track of the genes and changed coordinates (due to small INDELs) ? The ...
written 3 months ago by pixie@bioinfo1.3k
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Constructing nucleotide sequence after incorporating SNPs from SIFT file
... Hello, I have a file which gives me the position of the altered nucleotide or small insertion or deletion (reference allele and altered allele). Is there any tool which can be used to perform these changes on the reference nucleotide sequence and incorporate the ALT_ALLELE changes ? CHROM POS R ...
genome written 3 months ago by pixie@bioinfo1.3k • updated 3 months ago by finswimmer8.9k
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Structure Prediction of Transcription Factor and its binding site to a promoter element
... I have a wild type sequence of a transcription factor. I had predicted its structure using I-Tasser. I have a hunch that the structure might be a tetramer, although here I am getting it as a monomer here. What should I do in this case ? I know the sequence of the promoter element (DNA) to which it ...
structure written 4 months ago by pixie@bioinfo1.3k
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Answer: A: what next after DEGs?
... Networks may be? Study their interactions/associations , identify hub genes etc. ...
written 4 months ago by pixie@bioinfo1.3k
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Effect of amino acid mutation (deletion) on the protein structure
... I have a wild-type amino acid sequence of a plant. I have a mutated sequence with a single amino acid deletion. I have modeled the protein structure and computed the H-bonds and performed energy minimization using SPDV (swiss PDB viewer). Now, I need to delete a particular residue and perform the sa ...
protein mutation structure written 4 months ago by pixie@bioinfo1.3k • updated 4 months ago by RamRS20k

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