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What are the 4th and 5th column in ENCODE DNase enrichment files?

bed dnase encode chromatin accessibility written 4 months ago by hivemind • 10

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1.9k

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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 4.2 years ago by ashah90 • 30 • updated 16 months ago by Biostar ♦♦ 20

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865

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

assembly dnase encode coordinates written 2.8 years ago by eurioste • 20

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1.1k

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DNASE2TF + HOMER

homer dnase chip-seq rna-seq written 3.3 years ago by startup_biostar • 10 • updated 3.3 years ago by Satyajeet Khare • 1.5k

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919

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Overlap CNV with ENCODE DNAse-seq peaks

dnase encode dnase-seq cnv written 3.4 years ago by QVINTVS_FABIVS_MAXIMVS • 2.3k • updated 3.4 years ago by Sinji • 2.9k

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1.2k

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DNase data for GRCh38

dnase narrow peak broad peak open chromatin written 3.5 years ago by Adam Przedniczek • 30

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1.5k

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Map ENCODE DNaseI footprints to putative TFs

footprint dnase encode tf genomics written 5.4 years ago by enricoferrero • 780 • updated 5.4 years ago by Alex Reynolds ♦ 29k

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Recent Replies

C: Tips on: How to organise data on servers by ashok.ragavendran • 40
We have currently implemented a simple spec/tool for storing and managing our reference genome da...
C: Tips on: How to organise data on servers by flight505 • 10
Thanks for the upvote. When I started my PhD it was in a new location, I had zero experience with...
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Okay thanks, than `-s` is not necessary. The sample has the following header: #CHROM POS ...
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Thanks for reporting the issue. I could reproduce the error and think it is due to the whitespace...
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I've moved it to a `Forum` post as this is more a discussion than a question with a finite number...
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Great question! Also interested to hear from people. From my personal experience as an end user...
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Totally agree but error checking is a never ending issue :) Glad you figured it out.
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The read counts are not the average number per exon, they are close to the cumulative total, but ...
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but I checked the bbmap version for both the runs, and it's the same, since we haven't updated ou...
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You'll need some additional data, like 1000 Genomes data. While I am limited in my ability to pr...
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genomax are the read counts a cumulative total **or** average of the read counts of the ex...
C: bcftools consensus failure by grp2009 • 20
The `-s` option of `bcftools consensus` is meant for specifying the sample name (i.e. if the inpu...

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