User: rbronste

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rbronste50
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Posts by rbronste

<prev • 35 results • page 1 of 4 • next >
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Comment: C: awk code question
... Thank you, extremely helpful! ...
written 2 days ago by rbronste50
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Comment: C: awk code question
... ![enter image description here][1] [1]: https://dl.dropboxusercontent.com/u/105647823/Screen%20Shot%202017-03-27%20at%203.12.24%20PM.png So basically I am trying to modify the following command: zcat $dnase | awk '{if ($8 > 8) print}' | gzip > $dnase_gt8 The command is designed for the ...
written 2 days ago by rbronste50
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Answer: A: MACS2 Output for GREAT
... The easiest way is just to pull the data from the narrowPeak files, specifically the peak locations and then add the info required by GREAT, making a new TAB delimited txt file that you can then input into GREAT. ...
written 2 days ago by rbronste50
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awk code question
... Quick question for those that use awk often, what would the following command do to a narrowPeak file: awk '{if ($8 > 8) print}' Thanks ...
awk written 2 days ago by rbronste50 • updated 2 days ago by Pierre Lindenbaum91k
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Comment: C: Depleting BED file of specific regions
... So you would just use the intersect of BED file of promoter distal regions for lets say mm10? Thanks. ...
written 5 days ago by rbronste50
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Depleting BED file of specific regions
... Hi, Wondering about the best/easiest way to deplete a BED file of regions that are promoter proximal - or any other specific genomic "region"? Thanks Rob. ...
chip-seq sequencing written 5 days ago by rbronste50 • updated 5 days ago by Pierre Lindenbaum91k
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Running RSAT motif discovery on a computing cluster
... Hi, Wondering if anyone out there has experience installing and running RSAT on a cluster environment or running parallel jobs? Small batch motif finding is relatively fast with online tool but for large sets of intervals its a very slow process. Thanks. Rob ...
motif rsat chip-seq written 8 days ago by rbronste50
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Comment: C: Figure quality browser tracks
... Not really, that post is over 5 years old. ...
written 9 days ago by rbronste50
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Figure quality browser tracks
... Hi everyone, Wondering about consensus for the best approach to getting figure quality browser tracks, generally of bigwig files and maybe some conservation and ENCODE data in addition. Thanks. ...
sequencing ucsc igv browser written 9 days ago by rbronste50 • updated 8 days ago by Ben_Ensembl220
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Comment: C: Bed to BAM information transfer
... In this particular case its not so much crappy data just sparse due to the small cell population Im working with, I guess not uncommon with ATAC in general. ...
written 25 days ago by rbronste50

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