User: rbronste

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rbronste230
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Posts by rbronste

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Comment: C: Filtering fastq vs BAM for fragment size range
... This is a nice approach thanks, I guess my question was moreso if the two approaches (before and after alignment) would be equivalent in their final resulting bam file? ...
written 3 months ago by rbronste230
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Filtering fastq vs BAM for fragment size range
... Wondering if you would get equivalent results in limiting fragment size to a range by doing it at the bowtie2 level (mapping only that fragment range indicated by the -I and -X flags) or filtering of the resulting BAM file after alignment of all fragments? ...
bowtie2 fastq alignment bam written 3 months ago by rbronste230
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Comment: C: Filtration Of Reads With Length Lower Than 30 From Bam
... How would this be adjusted to give a BAM file with a range say 1-80bp for the insert size? ...
written 3 months ago by rbronste230
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Comment: C: MNase-seq / fragment size selection
... Also just curious what you're basing the 80bp on, like any particular papers/studies? Just wanted to take a look, as Im trying to also track down good boundaries to set. Thanks! ...
written 3 months ago by rbronste230
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Great tool, thanks for putting it together! My DEseqDataSet is actually a set of peaks instead of transcripts that all have a unique identifier going out to 6 figures, I was wondering if there was a way to use `selectLab()` to create custom labels such as TF names for factors I know to bind within ...
written 3 months ago by rbronste230
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Comment: C: Where can I find expression data for APOE gene in humans?
... You might try filtering/searching GEO datasets for the different ApoE isoform combos, though be careful averaging across datasets given their inherent differences in experimental design and approach to quantifying ApoE isoforms. e.g https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102956 ...
written 3 months ago by rbronste230
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Pulling out interval adjoining regions
... Looking for a good way to take a set of intervals and print out an interval set (bed file) that represents regions just upstream and downstream of every interval in the original file, lets say 10kb up and downstream. Any help appreciated, thanks! ...
bedtools bed bedops interval written 3 months ago by rbronste230 • updated 3 months ago by Alex Reynolds27k
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Comment: C: How can I correlate ATAC-seq peak signal with enhancer ChIP-seq mark signal (H3K
... Im not sure a correlation between read depth across ATAC and ChIP experiments is very informative, given how different the experimental techniques are (e.g. antibody based vs transposase). In general the amount of reads found in a ChIP experiment for something like a histone mark scales "linearly" w ...
written 4 months ago by rbronste230
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Comment: C: How To Randomly Sample A Subset Of Lines From A Bed File
... Do you know of a package or tool that assists in rejection sampling or would you script it out yourself? Thanks! ...
written 4 months ago by rbronste230
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Comment: C: How To Randomly Sample A Subset Of Lines From A Bed File
... One other quick thing, is it possible in this scenario to match the subsampled ~350bp peaks in their read counts to the target peak set? Im basically working with about 10K target peaks at some varying read depth and would like to take the downsampled 10K peaks across all chromosomes that I have at ...
written 4 months ago by rbronste230

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Popular Question 10 weeks ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Student 3 months ago, asked a question with at least 3 up-votes. For MEME vs. HOMER for de novo and known Motif finding
Popular Question 4 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
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Popular Question 5 months ago, created a question with more than 1,000 views. For Duplicates in ATAC-seq data
Popular Question 5 months ago, created a question with more than 1,000 views. For Calculating FPKM values from HT-counts
Popular Question 6 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 6 months ago, created a question with more than 1,000 views. For Calculating FPKM values from HT-counts
Popular Question 7 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 10 months ago, created a question with more than 1,000 views. For Removing PCR duplicates - fastq or BAM?
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