User: kennethcondon2007

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Posts by kennethcondon2007

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Comment: A: How reads are divided into taxonomy level in Qiime?
... This may help: https://www.youtube.com/watch?v=iy0JWgzmM_A ...
written 3 days ago by kennethcondon2007840
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Transmembrane domain protein structure
... Hello all, I need advice regarding the best tool for predicting transmembrane domain structure. I know transmembrane domain structures are a difficult niche. We have mutated a single position in a transmembrane domain that has produced a phenotype. We suspect the mutation is preventing binding with ...
transmembrane prediction protein structure written 4 days ago by kennethcondon2007840 • updated 3 days ago by cdsouthan1.7k
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Answer: A: bedtools what in B absent from A
... Maybe a bit clunky but: bedtools intersect -a A.bed -b B.bed -r -wao >out1.bed bedtools intersect -a B.bed -b A.bed -v >out2.bed cat out1.bed out2.bed | sort -k1,1 -k2,2n > outfinal.bed ...
written 5 days ago by kennethcondon2007840
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Comment: C: Picard tools duplicate removal
... Will the answer to this question influence your decision to use it or not in any way? ...
written 9 days ago by kennethcondon2007840
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Comment: A: Validating a mouse model with RNA-Seq
... Have you considered including time point d-1 and d0+4h? Cell-to-cell contact between pre-adipocytes is a factor in differentiation. At day 0, pre-adipocytes are likely to be fully confluent - so some expression changes may have already occurred. Also, I remember reading recently (sorry I cant find ...
written 10 days ago by kennethcondon2007840
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Comment: C: Analysis of gene expression
... "I have mapped a few reads to several reference genomes" - why? The only reference genome that is relevant is the genome of the species the data came from. ...
written 15 days ago by kennethcondon2007840
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Comment: C: Gene Expression Downstream Analysis
... 2017 Paper with an R package relevant to this type of analysis: [Pathway enrichment analysis approach based on topological structure and updated annotation of pathway.][1] [1]: https://www.ncbi.nlm.nih.gov/pubmed/28968630 ...
written 15 days ago by kennethcondon2007840
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Comment: C: expression to networking
... Well the basic principle of plotting a network of related genes is that you must try to plot a network of RELATED genes. So rather than passing a RANDOM gene set we first make a set of genes with something in COMMON (e.g. a differentially expressed gene set, or co-expression gene set, or tissue spec ...
written 21 days ago by kennethcondon2007840
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Comment: C: expression to networking
... First: Get the list of genes that are most significant deferentially expressed using a statistical package like [DESEQ2][1] Second: Pass the gene list to [StringDB][2] Third: Import the output of StringDB to [Cytoscape][3] [1]: https://bioconductor.org/packages/release/bioc/html/DESeq2.html ...
written 22 days ago by kennethcondon2007840
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Comment: C: Finding specific subsets of genes related with known transcription factors
... You say you have enriched TFBSs - To ensure we can answer your question, and to avoid any confusion with terminology and interpretation, can you tell us please how you got these "TFBSs"? It is more likely that you actually have a set of enriched motifs. If you do have the sites already.... then for ...
written 24 days ago by kennethcondon2007840

Latest awards to kennethcondon2007

Popular Question 3 months ago, created a question with more than 1,000 views. For RNA-seq RPKM significance cut off
Scholar 4 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Looking for an annotation tool
Student 4 months ago, asked a question with at least 3 up-votes. For Is annotation of enhancers to nearest gene pointless?
Good Question 5 months ago, asked a question that was upvoted at least 5 times. For Is annotation of enhancers to nearest gene pointless?
Student 5 months ago, asked a question with at least 3 up-votes. For Is annotation of enhancers to nearest gene pointless?
Appreciated 5 months ago, created a post with more than 5 votes. For Is annotation of enhancers to nearest gene pointless?
Popular Question 5 months ago, created a question with more than 1,000 views. For Better for my career: Degree in computer science or Phd in bioinformatics?
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Supporter 9 months ago, voted at least 25 times.
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Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Looking for an annotation tool

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