User: kennethcondon2007

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Posts by kennethcondon2007

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Comment: C: Diffbind results - non uniform width
... Thank you once again Rory :) ...
written 4 months ago by kennethcondon200710
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Diffbind results - non uniform width
... Hi all, I am running diffbind using narrowPeaks output from macs2 When using dba.count, I am taking each summit and counting reads +/-250 from the summit so I'm expecting to see in the diffbind report that the width column only contains "501" bindingmatrix <- dba.count(dbaobject, summits=250) ...
diffbind dba.count written 4 months ago by kennethcondon200710 • updated 4 months ago by Rory Stark2.0k
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Comment: C: Differential binding of ATAC-seq data with no replicates
... Hi Gordan, I really need to flesh this out a bit. It is quite a headache. So... 1) For downstream processing I need a consensus peak set. So ALL 32 samples must be merged. Then call peaks on the merged data to identify a consensus set of peaks. Then for each sample, count the number of 5’ read end ...
written 6 months ago by kennethcondon200710
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Comment: C: Differential binding of ATAC-seq data with no replicates
... Thank you Micheal - I was quite alarmed when I was informed there were no replicates, but there is nothing I can do about it now except remind them to include a bioinformatician during the planning stage. ...
written 6 months ago by kennethcondon200710
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Comment: C: Differential binding of ATAC-seq data with no replicates
... Thank you Gordon. That's my next read.   EDIT With 8 time points per condition, should I be pooling all 8 into a single file and peak call on that file? ...
written 6 months ago by kennethcondon200710
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Answer: A: DiffBind for ATAC-seq
... I can't be too clear on this answer but as I understand it MACS2 was designed for chip-seq and as such will always "shift" the reads in the 5' prime direction due to some detail in the production of the chip-seq data . We use the option --shift 100 to move ATAC-seq reads in the opposite direction so ...
written 6 months ago by kennethcondon200710
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Using Diffbind on ATAC data - adapter offset issue
... Hi,   I'd like to use Diffbind on Atac data. However what is done about the adapter adjustment that occurs before peak calling? For peak calling all forward reads are offset by +4 bases and reverse reads by -5 so aligning peak positons to BAM file positions of the reads may need reversing of the o ...
diffbind atac adapters written 6 months ago by kennethcondon200710 • updated 6 months ago by Rory Stark2.0k
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Differential binding of ATAC-seq data with no replicates
... Hi, I have ATAC-seq data for 8 time points of 4 conditions --> 32 samples in total. The only replicates I had were technical which were pooled early in the pipeline. There are no biological replicates. I have completed MACS2 peak calling and now want the differential binding (DB). I would like t ...
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Merging files with gene expression data
... Hi all, This seemed like such an easy task, yet I am boggled.   I have: 28 files: each named n.txt , where n is a type of tissue (e.g. cortex.txt, heart.txt) Each file contains 2 columns and the column headers are gene name (column 1) and log2rpkm (column 2) Each file contains around 30-40k ro ...
rnaseq merge files written 11 months ago by kennethcondon200710 • updated 11 months ago by jayme.rickman0

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