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Is strand important when it comes to DNAse and ChIP-Seq peak calling?

genome gene dnase chip-seq peak calling written 3.5 years ago by ashah90 • 30 • updated 7 months ago by Biostar ♦♦ 20

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MCS-R2 (encode HS-40) hg19 genomic coordinates

assembly dnase encode coordinates written 2.1 years ago by eurioste • 20

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952

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DNASE2TF + HOMER

homer dnase chip-seq rna-seq written 2.6 years ago by startup_biostar • 0 • updated 2.6 years ago by Satyajeet Khare • 1.3k

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Overlap CNV with ENCODE DNAse-seq peaks

dnase encode dnase-seq cnv written 2.7 years ago by QVINTVS_FABIVS_MAXIMVS • 2.2k • updated 2.7 years ago by Sinji • 2.8k

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DNase data for GRCh38

dnase narrow peak broad peak open chromatin written 2.7 years ago by Adam Przedniczek • 30

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Map ENCODE DNaseI footprints to putative TFs

footprint dnase encode tf genomics written 4.6 years ago by enricoferrero • 760 • updated 4.6 years ago by Alex Reynolds ♦ 27k

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Recent Replies

C: How to distinguish if a gene is a paralogue or an isoform? by Vitis • 1.9k
Not a typical bioinformatics question, but I'll give it a try. Probably both are true. This gene ...
C: Samtools: Question about filtering BAM file using flag by SDin • 0
I got it. Many thanks for your kind help!
C: Removing duplicated mutations from a txt by Friederike ♦ 2.5k
then: 1. read in the original file into R 2. use `unique(df)` 3. use that `dndscv` function and...
C: How to get short and sweet gene names/description for gene IDs? by BIOAWY • 110
Thank a heaps finswimmer :)
A: How to plot the output of bedtools genomecov as a histogram using gnuplot? by adynata • 0
if that data is in a file you could do plot'FILE' u (($3+$4)/2.):5:($4-$3) w boxes the location...
C: Parsing MEGAN blast2lca output by qinglong • 0
Thanks!!! But I also need to have a filtering based on the confidence score (cut-off: 50), do you...
C: MyCC not producing any bins by Kevin Blighe ♦ 37k
Thanks, but remember to use the `ADD REPLY` or `ADD COMMENT` button the next time when you post a...
A: MyCC not producing any bins by suran.nambisan • 0
Hi Kevin Thanks for your reply. The python version is given below: Python 2.7.13 :: Continuum An...
C: Removing duplicated mutations from a txt by F • 3.2k
Everything happened when I tried to remove duplicates; I run these package with original file suc...
C: MyCC not producing any bins by Kevin Blighe ♦ 37k
Hey Suran. No problem. For your first post, I have edited it and wrapped your text using the `101...
C: Automating Trimmomatic for total Noobs by new15b • 0
I do try to play with code, quite frequently in fact. The biggest obstacles I encounter are funct...
A: MyCC not producing any bins by suran.nambisan • 0
Hi Kevin. Sorry for late reply and sorry for the mess above. Is there a way to attach the log f...

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