User: ildem

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ildem20
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IGH - Montpellier
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1 month ago
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4 months, 3 weeks ago
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Posts by ildem

<prev • 13 results • page 1 of 2 • next >
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Answer: A: How to Find the Peak Summit Location for Broad Peaks in MACS?
... because the peaks are "broad". MACS2 assumes histone marks do not have a summit (unlike TF binding sites which have a summit at the point TF binds to DNA). you can try macs2 refinepeak to go back and generate summits. but they wont be too accurate for broad regions. ...
written 4 weeks ago by ildem20
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Answer: A: Homer motif analysis: "Very close % of target vs % of Background sequences with
... Hi, I usually get a decent enrichment over background, sometimes upto 3 fold, but at least a 1.5 fold would be expected. Can you give us your command line? What does your bedfile (input) look line? Could it be that you are searching for a motif in too large of an area? Usually you search for the ...
written 11 weeks ago by ildem20
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Answer: A: How do I find the readsets used to make refseq assemblies?
... You can try and start here perhaps: http://www.ebi.ac.uk/ena European Nucleotide Archive ...
written 11 weeks ago by ildem20
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Answer: A: Examining connectivity of specific genes in WGCNA
... yes, definitely. Keep in mind: 1. sample purity: if you are using tissues, differential composition of samples can drive artificial connections 2. Need to use RNA-seq from a similar batch (i.e. sequenced around the same time on the same machine, prepared by the same experimenter etc.) Otherwise t ...
written 11 weeks ago by ildem20
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Answer: A: bedtools mapbed assings 0 values eventhough mean is not zero
... Many thanks, Indeed the problems seems to be coming from the input files. In particular the Refseq bed files that I have downloaded from UCSC. It looks like if i cut out all the columns (RefseqID, strand etc.) and leave only the first three (chr, start, end), then it works fine. I have used bed f ...
written 11 weeks ago by ildem20
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bedtools mapbed assings 0 values eventhough mean is not zero
... Dear all, I am using Bedtools mapBed to assign mean Phastcon scores to regions. Phastcon scores are in bedgraph format and my command is: mabBed -a regions.bed -b scores.bedgraph -c 4 -n mean > out.txt The problem is, mapBed is assigning "0" for values that i know to be non-zero. I used se ...
bedtools mapbed assigns 0 written 12 weeks ago by ildem20
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Comment: A: SICER fails to run
... Hi, Indeed there was a problem with the genomedata.py. As you see the chromosomes spell our mm10-chroms :) thanks! ...
written 3 months ago by ildem20
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SICER fails to run
... Dear all, I am trying to run SICER on my files. I have done a bamToBed conversion and concatanated the files with cat. Command looks like: SICER.sh . merged.bed ctl.bam.bed . mm10 1 200 50 0.83 600 0.01 What Sicer does is it produces two big "removed" files and all the other files are em ...
fail to produce files sicer chip-seq bash written 3 months ago by ildem20
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bedtools closest gives a -1 distance with -io (ignore overlaps)
... I am using bedtools closest to find the closest feature to my peaks. I used unix sorted files (sort -k1,1 -k2,2n a.bed) my command line is bedtools closest -io -d -sorted -a a.bed -b b.bed This results in some features in a.bed to have -1 (no other negative value, only -1) distance. Since I ask ...
bedtools closest written 4 months ago by ildem20 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: plotProfile with mean of bigwig files
... thanks Devon, I was just wondering if i missed something.. ...
written 4 months ago by ildem20

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