User: kennethcondon2007
kennethcondon2007 • 840
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Posts by kennethcondon2007
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... This may help: https://www.youtube.com/watch?v=iy0JWgzmM_A ...
written 3 days ago by
kennethcondon2007 • 840
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... 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 ...
written 4 days ago by
kennethcondon2007 • 840
• updated
3 days ago by
cdsouthan • 1.7k
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... 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
kennethcondon2007 • 840
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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
kennethcondon2007 • 840
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... 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
kennethcondon2007 • 840
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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
kennethcondon2007 • 840
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... 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
kennethcondon2007 • 840
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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
kennethcondon2007 • 840
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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
kennethcondon2007 • 840
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... 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
kennethcondon2007 • 840
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