User: ildem

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ildem20
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IGH - Montpellier
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2 months, 3 weeks ago
Joined:
7 months, 3 weeks ago
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Posts by ildem

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Where can I get ?or how can I make a mappability track for hg38 assembly
... oh! thanks so much! I assumed i was missing an index file of some sort!! thanks again.. ...
written 12 weeks ago by ildem20
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Comment: C: Where can I get ?or how can I make a mappability track for hg38 assembly
... many thanks, I understand what the rn6.softmask.all.fa file is. I dont undestand what rn6.softmask.all file is (the line above) Are you saying they are the same thing? ...
written 12 weeks ago by ildem20
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Comment: C: Where can I get ?or how can I make a mappability track for hg38 assembly
... May i ask what exactly is this file? pref="rn6.softmask.all" # should be changed is it some sort of index? Did you generate it yourself? thanks.. ...
written 12 weeks ago by ildem20
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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 months 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 5 months 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 5 months 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 5 months 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 5 months 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 5 months 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 6 months ago by ildem20

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