User: sim.j.baum

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sim.j.baum50
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Posts by sim.j.baum

<prev • 17 results • page 1 of 2 • next >
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Comment: C: unit scale in plotprofile plot - deeptools2
... Thank you. Its a related question, but could probably fill a seperate question: RPKM vs RPGC? Both normalization methods are fine to use in the work stream performed above? ...
written 11 days ago by sim.j.baum50
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unit scale in plotprofile plot - deeptools2
... Hi all, I generated a plot via deeptools2 with the folliwing steps: BamCoverage to generate a bigwig file from my bam file with default conditions plus --normalizeUsing RPKM Next, i created a matrix at the regions of interest with computeMatrix and then used plotProfile to visualize this. ...
chip-seq deeptools2 written 11 days ago by sim.j.baum50 • updated 11 days ago by Devon Ryan92k
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Comment: C: MACS2 "total fragments in treatment" gives less number of fragments than expecte
... What was surprising to me is: > maximum duplicate fragments in treatment = 1 > Redundant rate in treatment: 0.99 which are very high. My guess is that you have lots of PCR duplicates in your library. Therefore, the majority of your fragments are filtered out, I think. But lets wait ...
written 16 days ago by sim.j.baum50
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Answer: A: DiffBind to call differential binding of Super-enhancers from ROSE
... I think I know what you mean: I used deeptools2 for that - and it is similar to figures published by Loven J. et al. 2013 in Cell I think - they show the difference of the average binding in different conditions at SE and normal enhancer. If so you take A.) the BED SE file and get the median or ...
written 21 days ago by sim.j.baum50
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Comment: C: Which one to use for ChipSeq replicate comparison: Spearman or Pearson
... Very nice answer. What you can also do is to select `multiBamSummary BED-file --BED selection.bed --bamfiles file1.bam file2.bam -o results.npz` and use a BED-file if you have already genomic regions of interest. ...
written 21 days ago by sim.j.baum50
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Answer: C: deep learning predict gene expression
... A very interesting topic IMO. I think there is no easy answer to your question because you would need a lot of multi-dimensional data to say that element A is regulating gene B - and you would need functional validation with wet-lab experiments. However, what came to my mind is ChromHMM (http://comp ...
written 21 days ago by sim.j.baum50
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Comment: C: DiffBind without replicates
... See answer from Devon Ryan below. In the mean time while creating new data with replicates you could use bedtools to intersect regions between both ChIPseq exerpiemtns and identify regions mutually exclusive. Take the binding intensity differences into account. Validate those regions and differen ...
written 27 days ago by sim.j.baum50
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Comment: C: Question about implementing quality control of TCGA data for survival analysis
... "What would it mean if they stay separated in PC2, PC3 for example?" That there is a higher variance between this group of samples and the others - Arguing for a broader diversity and maybe multiple factors playing a role. "many subtypes so that is what I am starting to think may be the cause" - Y ...
written 3 months ago by sim.j.baum50
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Comment: C: How to filter "only Mrna "s from total RNA ?
... nicely explained here IMO: https://reasoniamhere.com/2013/09/16/awk-gtf-how-to-analyze-a-transcriptome-like-a-pro-part-1/ ...
written 3 months ago by sim.j.baum50
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Comment: C: Question about implementing quality control of TCGA data for survival analysis
... Are those samples also popping up as a separate group in the next principal components? Consider that you are looking at 16% of variance explained within the data. What kind of tumor types are you looking at? In prostate cancer you can have several sub-types (e.g.: TMPRSS2_ERG fusion). Or, are the s ...
written 3 months ago by sim.j.baum50

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