User: rbronste

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rbronste140
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Posts by rbronste

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Comment: C: Eliminating repetetive motifs found by MEME
... Great suggestions. Do you know of a good source to obtain a mouse (mm10) bed file of repeat-masked regions? UCSC I guess? ...
written 8 days ago by rbronste140
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Eliminating repetetive motifs found by MEME
... Whenever I run MEME I get several top E-value hits that are pure repeats (often 25bp or longer) and I would like to eliminate these from the search and keep only actually possible TF motifs. Is there a way to do this? Thanks. ...
motif meme chip-seq written 8 days ago by rbronste140 • updated 8 days ago by Alex Reynolds20k
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MEME motif width
... When putting such a command into MEME: meme *.fa -maxsize 1000000 -dna -minw 8 -maxw 25 -nmotifs 1 It splits up what its looking for into 8, 11, 15, 21 and 25 My question is whether it is looking between those sizes for any motifs that range lets say between 11 and 15 or only looking for those t ...
chip-seq meme motif written 9 days ago by rbronste140
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Comment: C: Motif database of choice
... Yes Ive tried a number of them, currently using RSAT but have gone through HOMER (slightly outdated) and MEME. ...
written 14 days ago by rbronste140
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Motif database of choice
... Wondering what people working with mouse and human samples prefer, since there are so many choices from Jaspar to cisBP - interested in what is standard out there, especially for mouse? Thanks. ...
motif rsat chip-seq written 14 days ago by rbronste140 • updated 14 days ago by jared.andrews0790
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Masking repeats in ATAC-seq data
... Wanted to get some opinions about masking repeats during differential peak calling for ATAC-seq or other open chromatin datasets, is this advised and if so what is a good strategy? Thanks. ...
repeats atac-seq deseq written 17 days ago by rbronste140
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Comment: C: Comparing open chromatin data to ChromHMM model
... No this is actually mouse data. ...
written 6 weeks ago by rbronste140
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Comment: C: Normalizing Illumina fastq read-lengths from different GEO datasets
... Is there a particular PCA tool you would use for this instance? ...
written 7 weeks ago by rbronste140
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Comment: C: Normalizing Illumina fastq read-lengths from different GEO datasets
... I have not approached the problem via PCA yet, however that is a good idea as well. I just assumed that when datasets from different sources are repurposed for ones study (right from the fastq files in GEO), the differing read lengths off the Illumina machine would present some coverage confound whe ...
written 7 weeks ago by rbronste140
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Normalizing Illumina fastq read-lengths from different GEO datasets
... When dealing with fastq files from different datasets in the literature which may be comprised of read lengths such as 50bp or 75bp etc., is there a good way to normalize across them with your own data for comparison in mind - before/after alignment? Thanks. ...
geo fastq rna-seq written 7 weeks ago by rbronste140

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