User: jamzaleg84

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jamzaleg8440
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Posts by jamzaleg84

<prev • 7 results • page 1 of 1 • next >
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Deeptools heatmap analysis - graphing unique clusters of heatmap
... Hello, I used deeptools to make a heatmap of a ChIP-seq experiment with 4 samples - WT_TF1, WT_TF2, Mutant_TF1, and Mutant TF2. I made the heatmap referenced to a bedfile of all unique peak sites for all the conditions. I used the --kmeans option of plotHeatmap in an attempt to do a clustering anal ...
plotheatmap deeptools computematrix written 2 days ago by jamzaleg8440 • updated 2 days ago by Devon Ryan95k
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Comment: C: plotHeatmap for clustering samples
... Hello! I decided to narrow down the list to one mutant and one WT with Pulldowns for TF1 and TF2. As you suggested I made the interval 1kb upstream and downstream the unique called peak site for all conditions. When I call for clustering in the plotHeatmap command it makes nice clusters, but it clea ...
written 2 days ago by jamzaleg8440
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Comment: C: plotHeatmap for clustering samples
... Thank you so much! Yes, sorry I probably should have asked this as a separate question, but it was a natural follow-up question to the point you made about maybe the pull-downs not working. Thank you so much for all your help! Yonatan ...
written 4 days ago by jamzaleg8440
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Comment: C: plotHeatmap for clustering samples
... Thank you so much for your reply! I re-did the computeMatrix with the original TF union file (without the Slop) and added 1kb to both ends (picture below). I also looked at all the files (including the inputs) corresponding to all the genes to see if there is any difference between the pull-down and ...
written 5 days ago by jamzaleg8440
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Comment: C: plotHeatmap for clustering samples
... Hi there, Thank you for your response. Do you mean you would like me to post the actual files I used to make the graph? Certainly, but my question was more based on whether or not I made the appropriate reference-point list to do the heatmap-cluster analysis. Or should I have used a different refe ...
written 7 days ago by jamzaleg8440 • updated 5 days ago by RamRS27k
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plotHeatmap for clustering samples
... Hello Everyone, I've been using deeptools to make heatmaps of ChIP-seq samples and hierarchical clustering of those samples. I have two different transcription factors that I'm interested in and I'm interested in determining if there are regions where each transcription factor binds individually, w ...
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filter patients based on specific mutation using TCGAbiolinks
... Hello Everybody, I have a question about TCGAbiolinks that I didn't see anyone else address (please make me aware if I'm incorrect). My goal is to identify within TCGA-BRCA a specific mutation of interest and find all barcodes for breast cancer patients harboring this mutation and place it into a l ...
tcgabiolinks tcga mutation gdcquery written 14 months ago by jamzaleg8440

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