User: kennethcondon2007

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Posts by kennethcondon2007

<prev • 175 results • page 1 of 18 • next >
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Comment: C: Uploading sequencing data from GEO to USCS Genome Browser
... We need to know the file types you are trying to upload... chip peaks wont show up as peaks in a bed file (.bed) unless you make a signal track bedgraph file (.bdg). If you are happy to see blocks instead of peaks then stick to bed files (boring). Bed files and Bedgraph files are too big to be usefu ...
written 2 hours ago by kennethcondon2007530
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Answer: A: How can I check for library composition bias RNA-seq data
... Run [FASTQC][1] + [MULTIQC][2] initially to look for things like GC bias and overrepresented sequences. You should know when your library was fragmented from the RNA-seq method. That will give a clue as to which end may be lower quality. QC will help with identifying this and knowing what to trim. A ...
written 4 hours ago by kennethcondon2007530
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Heatmap - with diagonally split tiles
... Hi all, I'd like to create a heatmap in which the individual cells are split diagonally so that: 1 - each cell can contain 2 colours 2 - different colours can be assigned based on category 3 - different shades can be applied based on a numerical scale I'm not even sure what terms are used to se ...
split heatmap written 6 hours ago by kennethcondon2007530
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Comment: C: Finding Primary Motif from Genomic DNA data
... cheers thanks :) Ill give it a try. ...
written 9 hours ago by kennethcondon2007530
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Comment: C: How to compare peaks (called by MACS2) within a specific genomic area for two sa
... Im working on ATAC-seq data at the moment. I've used [ChipPeakAnno][1] to annotate the peaks in the narrowPeaks file (MACS2 output) for genomic features (TSS etc). You could then do a simple count of the number of peaks annotated for each feature. Have you considered using [DESEQ2][2] for getting ...
written 11 hours ago by kennethcondon2007530
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Comment: C: Compare pairs of key/value of perl hash tables
... list::compare is great ...
written 1 day ago by kennethcondon2007530
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Comment: C: Is annotation of enhancers to nearest gene pointless?
... Thanks i.sudbury "I'm not sure I follow your suggestion."....If the TFs (edges), could link an enhancer (node1), with a gene (node2) that it is known to regulate from other data. yeah, questionable. Time to get the books out on TADs. I do like the suggestion of pairing enhancer and gene state chan ...
written 1 day ago by kennethcondon2007530
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Comment: C: Is annotation of enhancers to nearest gene pointless?
... ha! I was looking for that :) ...
written 1 day ago by kennethcondon2007530
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Comment: C: Is annotation of enhancers to nearest gene pointless?
... Thank you for the correction pld :) ...
written 1 day ago by kennethcondon2007530
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Comment: C: Is annotation of enhancers to nearest gene pointless?
... Great reply thank you So this leads on to asking how to approach enhancer annotation. I have not done a comprehensive search for tools that annotate but my impression is CRE annotation packages usually just annotate the nearest gene. Surely ideally to have any great confidence requires some form ...
written 1 day ago by kennethcondon2007530

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Good Question 1 day ago, asked a question that was upvoted at least 5 times. For Is annotation of enhancers to nearest gene pointless?
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Appreciated 1 day ago, created a post with more than 5 votes. For Is annotation of enhancers to nearest gene pointless?
Popular Question 23 days 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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