User: aw_gibbs

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aw_gibbs0
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Posts by aw_gibbs

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How to find transcription factor downstream binding
... Hi all, I would like to find out what the mouse Stat3 transcription factor **binds** to and the full signalling pathway(s) that it is involved in. So far, I have only managed to find a signalling pathway that ends in Stat3, and subsequently genes that bind to Stat3. I have tried JASPAR, but the w ...
gene rna-seq written 5 months ago by aw_gibbs0 • updated 3 months ago by Biostar ♦♦ 20
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GSEA with mouse RNAseq data
... Hi everyone, I have had RNAseq performed on mouse samples (12 samples, 4 groups) and have the results ready to plug into Gene Set Enrichment Analysis (GSEA) software. I notice that there are plenty of human gene sets available on MSigDB, but not many for mouse. I would like to run GSEA with 6 sign ...
rna-seq written 6 months ago by aw_gibbs0 • updated 6 months ago by Buffo1.7k
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Comment: C: E coli Sequencing & Analysis
... Thank you very much for your reply! I think I will try both methods (SPades&Prokka, NCBI tools) and see which ones I get on with most. ...
written 10 months ago by aw_gibbs0
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E coli Sequencing & Analysis
... Hello, I have been given the task of assembling a 'new' Ecoli genome and analysing the genes present etc. The Ecoli is a new strain, and has been taken and run on a Nextseq 500 in high-output mode with 150bp paired end reads. The 'raw' files that I have is the forward and reverse reads. I have i ...
genome assembly alignment sequencing written 10 months ago by aw_gibbs0 • updated 10 months ago by rebeccarenberg20
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Remove Probes from Raw .CEL Files - AFFY HG-U133-Plus2.0
... Hi all, I have multiple Accessions(13) that I'm combining to analyse data(~2000 samples). All of the Accessions have the same platform (GPL570). After investigating all the Accessions, I noticed that one of them (E-MTAB-3444) has around 300 extra probes added to the platform. This means that I can ...
R rna-seq written 2.7 years ago by aw_gibbs0

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