User: pixie@bioinfo

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pixie@bioinfo1.1k
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PhD Student

Posts by pixie@bioinfo

<prev • 141 results • page 1 of 15 • next >
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Comment: C: How to plot Z-scores in R for gene expression data
... Thank you so much,I finally could do it. You saved a lot of time for me ! ...
written 17 days ago by pixie@bioinfo1.1k
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Comment: C: How to plot Z-scores in R for gene expression data
... Actually, MultiExperiment Viewer (MeV) creates clusters and then we can visualize plots. Here, I have already clustered my data and wish to visualize ...
written 17 days ago by pixie@bioinfo1.1k
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Comment: C: How to plot Z-scores in R for gene expression data
... Thanks, am looking into it. ...
written 17 days ago by pixie@bioinfo1.1k
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How to plot Z-scores in R for gene expression data
... Hello, I have a table with gene expressions across samples. I have calculated the z scores and need to create this plot as given below: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022196#pone-0022196-g001 My table looks like: `Gene_name E_2401_ctrl_1 E_2401_ctrl_2 E_2401_ctr ...
gene expression written 17 days ago by pixie@bioinfo1.1k • updated 17 days ago by rice.researcher60
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Comment: C: Regarding getting gene count tables for DeSeq from StringTie using prepDE.py
... Thank you for the reply. What I had meant was, most of my gene IDs are missing in the gene count tables and are replaced with the StringTie IDs (MSTRG). When I looked into the merged gtf file, I saw that the gene ids (of the transcripts) are not present in the count table, rather the MSTRG IDs are ...
written 28 days ago by pixie@bioinfo1.1k
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Regarding getting gene count tables for DeSeq from StringTie using prepDE.py
... Hello, I followed the pipeline for StringTie and prepDe.py as given exactly from the ballgown directory created as given in http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#de However, majority of the transcript IDs given in the StringTie merged file are not present in the gene count tab ...
stringtie rna-seq written 4 weeks ago by pixie@bioinfo1.1k • updated 28 days ago by Satyajeet Khare1.0k
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Comment: C: Help regarding RNA-seq STRINGTIE pipeline and output
... Thanks for the input ...
written 3 months ago by pixie@bioinfo1.1k
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Comment: C: Help regarding RNA-seq STRINGTIE pipeline and output
... Thanks for your input, will look into it. ...
written 3 months ago by pixie@bioinfo1.1k
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Help regarding RNA-seq STRINGTIE pipeline and output
... Hello, I have started working on RNA-seq data. I have samples at 0th hr (control, 2 replicates ), and 4 other time points, each with two replicates. I have two objectives. 1) Construct a network using WGCNA across all samples including replicates 2) Identify differentially expressed genes for each ...
stringtie rna-seq written 3 months ago by pixie@bioinfo1.1k
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Comment: C: HISAT error: Encountered internal HISAT2 exception (#1)
... Thanks, I'll try out. Yea, it was a typo, corrected it ...
written 3 months ago by pixie@bioinfo1.1k

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