User: reskejak

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reskejak20
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Location:
Michigan State University
Website:
https://github.com/res...
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5 months, 1 week ago
Joined:
1 year, 5 months ago
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r*******@msu.edu

Posts by reskejak

<prev • 8 results • page 1 of 1 • next >
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Clarity for proper design model matrix with paired sample analysis
... I have done a significant amount of reading over the past few days and am still uncertain about proper model matrix design for paired sample analysis. I am starting with a limma/voom object `v` that I would like to assess for transcriptional differences via RNA-seq between disease subtypes and their ...
R design limma rna-seq statistics written 7 months ago by reskejak20
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Answer: A: What is the difference between "findMotifsGenome.pl" and "findMotifs.pl" in home
... The answer lies within your own explanation! You will want to use findMotifsGenome.pl by supplying a HOMER-ized BED file (see manual). This will identify enriched motifs from the ChIP peaks you empirically determined. The alternative, findMotifs.pl, is useful for seeking underlying regulatory patte ...
written 16 months ago by reskejak20
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Answer: A: csaw - Htslib import errors and missing reads/chromosomes
... **UPDATE: ANSWER** I have not exactly identified the cause of this `Rhtslib` error, but I tried many alternative and repeated methods to generating these BAMs from scratch to no avail. This was ultimately remedied by using `csaw` on a Centos cluster with >100 gb RAM. I have not tried submitting ...
written 17 months ago by reskejak20
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csaw - Htslib import errors and missing reads/chromosomes
... I'm working through `csaw` for paired-end ATAC-seq data (see [my other post][1] for more background on my general workflow), and I don't think my BAM files are being properly read into R. I have used numerous files that are coordinate-sorted (also have tried name-sorted) and indexed (via either `sam ...
csaw bam chip-seq atac-seq library written 17 months ago by reskejak20 • updated 4 months ago by xuzhougeng0
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Answer: A: Library complexity downsampling validation and samtools flagstat (ATAC-seq)
... **UPDATE:** Shortly after documenting all of this *on paper*, I realized I should be hard-filtering the mtDNA and unmapped reads from the libraries, as they may be still included in library size calculations even if they are not used. I revised my method to completely remove these reads and only re ...
written 17 months ago by reskejak20
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Library complexity downsampling validation and samtools flagstat (ATAC-seq)
... I have been trying to downsample my ATAC-seq libraries to normalize across all samples within my experimental design using `ATACseqQC::readsDupFreq|estimateLibComplexity`, which is based on the established `preseqR::ds.mincount.bootstrap` framework. After scaling all libraries to the same predicted ...
atac-seq samtools complexity atacseqqc library written 17 months ago by reskejak20
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Batch and combining reads from two flow cells for the same ChIP/ATAC-seq library
... I'm sure this has been answered previously, but I have been unable to find a directly-similar question here for ChIP-seq (or similar) data. We have a library which has been sequenced twice, on two flow cells, corresponding to one biological replicate sample from an experiment (each flow cell is an ...
illumina combine atac-seq chip-seq batch written 17 months ago by reskejak20 • updated 17 months ago by Devon Ryan93k
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DiffBind - normalization methods with biologically-relevant differences in signal-to-noise
... I have been using DiffBind for differential-accessibility analysis with ATAC data and encountered the seemingly infamous normalization issue: our results are very different when normalizing by full library read depth as opposed to depth of reads within consensus peaks (from my understanding of how b ...
normalization diffbind atac chip-seq signal written 17 months ago by reskejak20 • updated 17 months ago by Devon Ryan93k

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