User: varsha619

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varsha6190
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Posts by varsha619

<prev • 39 results • page 1 of 4 • next >
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Comment: C: bedGraphToBigWig error - end coordinate bigger than chr
... Fixed it with bedClip, thank you for your help! ...
written 11 days ago by varsha6190
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bedGraphToBigWig error - end coordinate bigger than chr
... Does anyone know a way to fix the bedGraphToBigWig error - end coordinate bigger than chr? My input is a bedGraph generated using MACS2. This link suggests using bedClip - https://groups.google.com/forum/embed/#!topic/macs-announcement/gXdf115Xy5Q. But I would like to know if there is a command lin ...
macs2 bedgraphtobigwig written 24 days ago by varsha6190 • updated 24 days ago by Alex Reynolds19k
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Visualize smooth ChIP peaks with Homer makeUCSCfile
... Hello, I am trying to use Homer makeUCSCfile for my ChIP seq data using as follows - makeUCSCfile sample.tagdir/ auto -style chipseq > sample.bedGraph.gz Although I am able to visualize the ChIP peaks in UCSC, I would like to get a smoothened plot instead, please let me know if there is a ...
homer chip-seq ucsc written 5 weeks ago by varsha6190 • updated 14 days ago by Biostar ♦♦ 20
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Comment: C: phastcon conservation score for chip seq peaks
... I used these steps to get my phastcons scores - 1. Get the bw file from UCSC 2. Convert bigWigToBedGraph and bedGraph to bed (awk '{print $1 "\t" $2 "\t" $3 "\t" $4}') 3. bedtools intersect -a ChIP_peaks.bed -b phastCons.bed Is this the best way to do this? My final goal is to plot a PhastCons sc ...
written 3 months ago by varsha6190
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Comment: C: How To Calculate Conservation Score Of Given Bed Regions
... I used these steps to get my phastcons scores - 1. Get the bw file from UCSC 2. Convert bigWigToBedGraph and bedGraph to bed (awk '{print $1 "\t" $2 "\t" $3 "\t" $4}') 3. bedtools intersect -a ChIP_peaks.bed -b phastCons.bed Is this the best way to do this? My final goal is to plot a PhastCons sc ...
written 3 months ago by varsha6190
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Comment: C: phastcon conservation score for chip seq peaks
... Does anyone know an equivalent of http://ceas.cbi.pku.edu.cn/submit.htm for species other than mice and human? ...
written 3 months ago by varsha6190
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Comment: C: phastcon conservation score for chip seq peaks
... Thanks @Alex Reynolds, I was wondering if there is any existing program available for what your in-house perl script does? ...
written 3 months ago by varsha6190
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phastcon conservation score for chip seq peaks
... Hi, I would like to do get conservation scores for my ChIP-seq peaks. Is phastcon the best method to use? I have read the following threads but am still not sure what is the best way to go about this - https://www.biostars.org/p/65972/ https://www.biostars.org/p/15398/ I would like to compare b ...
phastcon chip-seq written 3 months ago by varsha6190
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Comment: C: meme mast for overlapping sequences
... Does anyone know of a different software I can use for obtaining a list of motif match hits that include overlapping regions? ...
written 5 months ago by varsha6190
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meme mast for overlapping sequences
... Hi, I am using meme mast suite for motif scanning and the manual says that mast only gives output of non-overlapping sequences. I feel like I might be missing some potential motif hits because of this and was wondering if there is a way to make mast output the overlapping hits as well? I apprecia ...
meme motif mast written 5 months ago by varsha6190

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files

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