User: rbronste

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rbronste200
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Posts by rbronste

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Errors with samtools depth on merged bam file
... After merging 6 bam files (samtools merge) I attempted to look at the read depth within a specific set of intervals and got the following error, not sure exactly why expect maybe the merge tool takes a sam and not a bam file? samtools depth -b --bed /sonas-hs/tollkuhn/hpc_norepl/home/rbro ...
bam samtools sam written 8 hours ago by rbronste200 • updated 7 hours ago by Vijay Lakhujani3.2k
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Read depth interval comparison
... I was wondering about a good method to compare read depth at specific positions (bed file intervals) between two bam files and get as an output the depth across both bam files next to each interval in question? Thanks! ...
read depth bed bedops bam bedtools written 14 hours ago by rbronste200 • updated 13 hours ago by Pierre Lindenbaum114k
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Extending BED intervals
... Kind of a straightforward question, but what is a quick/simple method to take a bed file with an avg bp size of 350 and extend every interval by 325bp in each direction? Thanks! ...
bedtools bed bedops interval written 1 day ago by rbronste200 • updated 1 day ago by Alex Reynolds26k
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Panther pathway gene list counts
... I was wondering whether there was a way to see the total number of genes that make up every panther pathway category? Just wondering about relative enrichment and if its just an artifact of vastly different numbers of genes that comprise every category? Thanks! ...
panther gene ontology pathway analysis go written 1 day ago by rbronste200 • updated 1 day ago by c.chakraborty100
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Plotting motif enrichment
... Just thinking about different ways one could visually represent motif enrichment in target peak set over control, with significant points on the plot being marked with motif PWMs, if anyone can point me to a publication or some interesting code it would be much appreciated. Thank you! ...
ame meme motif pwm written 5 days ago by rbronste200
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Comment: C: How To Randomly Sample A Subset Of Lines From A Bed File
... Perfect, thanks! Second option is what I am looking for in this instance. ...
written 5 days ago by rbronste200
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Comment: C: Parsing AME tsv file
... Ok figured it out seems to work like this for true positive intervals with specific motifs IDs: grep -v ^motif sequences.tsv | grep -w tp | grep -w MA0258.2 | cut -f 2,3,6 | cut -d '_' -f 1 | tr ":-" "\t" | head MA0258.2 chr12 15566967 15567317 tp MA0258.2 chr11 88155633 88155983 tp ...
written 5 days ago by rbronste200
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Comment: C: Parsing AME tsv file
... Maybe a hint? :) Not as familiar with awk, though trying to learn. ...
written 5 days ago by rbronste200
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Comment: C: Tool to predict Enhancer gene target
... Actually GREAT now has an R package associated with it, which I find much more useful than the web interface. [https://bioconductor.org/packages/release/bioc/html/rGREAT.html][1] ...
written 5 days ago by rbronste200
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Comment: C: How To Randomly Sample A Subset Of Lines From A Bed File
... I guess I can also take the aggregate bed files representing all chromosomes before downsampling and simply subsample intervals of 350bp in length and thereafter use your approach at the start of this thread to subsample those evenly across all chromosomes? Is there an easy way of taking just a BED ...
written 5 days ago by rbronste200

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Popular Question 3 days ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
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