User: groupelmarwolf

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Posts by groupelmarwolf

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Comment: C: Deeptools Sorting for score values
... Perfect ! Works like a charm ! :) Thanks for the excellent advice. ...
written 2.5 years ago by groupelmarwolf0
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Comment: C: Deeptools Sorting for score values
... Thanks Devon for your response ! I am trying to plot Pol2 ChIP Seq but sorted for histone marks. So I have a BED file(or bedGraph) with histone mark tags in the 4th column. I would like to make a heat map of Pol2 (so i take the Pol2 ChipSeq bam file, sorted and indexed as per the chromosome numbe ...
written 2.5 years ago by groupelmarwolf0
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Deeptools Sorting for score values
... I am having a scored bed file with weighted values in the 4th column. I want to use this scored file to as a sorting parameter for another .bam file. However, the input to computeMatrix operation allows only bigWig files to be used in -S option...and creating bigWig files required indexing based on ...
deeptools sorting heatmaps written 2.5 years ago by groupelmarwolf0 • updated 2.5 years ago by Devon Ryan92k
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Comment: C: Issue: Scaled Region heat map using Deeptools 2.0 showing no signal, same files
... Nothing. It gives me the same output. But when I give smaller regionBodyLength, it works. Maybe I should have played around a bit more before posting :/ Thanks for super quick response. ...
written 2.8 years ago by groupelmarwolf0
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Issue: Scaled Region heat map using Deeptools 2.0 showing no signal, same files and parameters give excellent heat map around TSS.
... I tried to create a heat map using computeMatrix reference-point which gave excellent result: computeMatrix reference-point -a 2500 -b 2500 -bs 5 -p max --sortRegions no -R /home/Data/reference/RefSeq_All.BED -S loucy_input_sorted.bw -out input_sorted_loucy_wg.txt.gz plotHeatmap -m input_ ...
heat-maps deeptools chip-seq written 2.8 years ago by groupelmarwolf0

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