User: piyushjo

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piyushjo170
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Posts by piyushjo

<prev • 83 results • page 1 of 9 • next >
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Comment: C: Single cell clutering after regressing out cell cycle effect using seurat
... Did you PCA plot cells by there S, G2M and G1 score and saw different cluster for each stage like Fig 3 in tutorial? If yes, then it suggest that cell cycle genes have significant input to variation. If not then they don't, in that case regressing wouldn't make any difference. If you did see differe ...
written 6 weeks ago by piyushjo170
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Comment: C: HISAT2 index building
... I am not an expert but I did get an opinion from a person who provide core services at the NIH, that you need to be have the transcriptome GTF for building the index. Do it without the exon information and it will be fine. You will be using the annotation file while quantifying. I am doing exactly ...
written 7 weeks ago by piyushjo170
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Comment: C: lncRNA and circular RNA identification softwares
... Any annotation, whether RefSeq or GENCODE already includes bunch of lncRNAs. You can use biomaRt package to figure out which of the gene id's belong to lncRNA class. If you looking for novel lncRNAs, those that are not annotated yet, there are bunch of papers you can follow. https://www.nature.c ...
written 8 weeks ago by piyushjo170
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Comment: C: How to filter out the non-coding genes?
... Use the biomaRt vignette. If you have ids as ensembl gene ids it is pretty easy. Let x be a character array with your ensembl gene ids (with and without version information) goids = getBM(attributes = c('ensembl_gene_id', 'gene_biotype'), filters = 'ensembl_gene_id', ...
written 9 weeks ago by piyushjo170
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Comment: C: scRNA-seq analysis of two data-sets
... Thanks for your insight! ...
written 9 weeks ago by piyushjo170
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Comment: C: scRNA-seq analysis of two data-sets
... Ok I understand your clarification, but what would you suggest doing when I really want to find something that connects the two sets that I know for sure are overall different. For example, if I have a differentiating neuronal culture from Day 1 and Day 2 and I am really interested in finding the tr ...
written 9 weeks ago by piyushjo170
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scRNA-seq analysis of two data-sets
... Hi, So I have two datasets from two different yet related cell lines: pre and post relapse cancer cell line from same patient. I have performed single cell sequencing for both of them with the hypothesis that I will be able to find rarely expressed cells in either that are key to becoming relapse. ...
scrna-seq seurat written 9 weeks ago by piyushjo170 • updated 9 weeks ago by jared.andrews073.7k
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Comment: C: Single cell clutering after regressing out cell cycle effect using seurat
... Ok Thank you for your explanation. ...
written 9 weeks ago by piyushjo170
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Single cell clutering after regressing out cell cycle effect using seurat
... Hi, I am using cancer cell line scRNA-seq data to fing rarely expressed cells in homogenous cell culture. I am following seurat vignette for clustering. I also fund the seurat tutorial to regress out cell cycle genes effect. However, I have a basic question. My current work is as follow: 1) Find v ...
scrna-seq seurat clustering written 9 weeks ago by piyushjo170 • updated 9 weeks ago by Haci160
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Comment: C: Extracting important gene with similar expression level from multiple samples
... Follow the example in the link below. It will help you get correlated gene cohorts and also do some trait relationships. There are also tutorials on the first link (ucla.edu), but I find the tutorial below much easier to understand. https://wikis.utexas.edu/display/bioiteam/Clustering+using+WGCNA ...
written 11 weeks ago by piyushjo170

Latest awards to piyushjo

Popular Question 10 weeks ago, created a question with more than 1,000 views. For How different is rlog transformation from vst transformation in DESeq2
Scholar 12 weeks ago, created an answer that has been accepted. For A: Get a bunch of ENTREZID into gene symbols
Popular Question 6 months ago, created a question with more than 1,000 views. For How different is rlog transformation from vst transformation in DESeq2

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