Moderator: seidel

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seidel7.1k
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I work as a scientist at a non-profit research institute.

Posts by seidel

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Answer: A: Bedtools to make a bed file for promoter
... You're not getting any output because your BED file is not the correct format. You have strand in the 5th column, but BED format has strand in the 6th column. 1 chrom 2 chromStart 3 chromEndchromStart. 4 name 5 score Score between 0 and 1000 6 strand You can substitute a pe ...
written 6 weeks ago by seidel7.1k
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Comment: C: biological sequences random seq
... You'll have to give more context for a meaningful answer to this. A simple interpretation would be: a parent sequence if mutated, will give rise to derivative sequences. So if you mutate some percentage of the bases, it will give rise to a number (m) of derivative sequences. So...what is the context ...
written 6 weeks ago by seidel7.1k
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Comment: C: Working in R with HTS cluster analysis data
... Try your workflow on a toy sample of your data. For instance, if you could take a 20% of your data, would it work? Load the data, take a sub-sample, destroy the original object followed by gc() to clear memory. If it doesn't work, take a smaller sample. If it does work, examine how many resources we ...
written 6 weeks ago by seidel7.1k
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Answer: A: How to compare two sets of results from Limma?
... The simple approach: Select DE genes from each data set and examine their overlap via Venn diagram. Do genes DE overall overlap? Do genes in each category (up, down) overlap? You can evaluate the significance of overlap using a hypergeometric distribution or fisher test (see the help for phyper() if ...
written 10 months ago by seidel7.1k
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Comment: C: GRanges: merge metadata from the same ranges
... Maybe some information is required as to what exactly you're trying to accomplish. If the ranges will be identical between each GRanges object you are creating, then you already have a set of reference ranges on which to score each tool, and each GRanges instance contains the results for that tool, ...
written 12 months ago by seidel7.1k
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Comment: C: how to compare the difference of read counts in a given region
... Sorry about that. I updated the references. ...
written 12 months ago by seidel7.1k
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Answer: A: Euclidean Clustering and pattern confusion
... Your graphic is cut off - so we can only see what's happening in the top portion of your heat map - but assuming the pattern is preserved in the unseen portion, the simple answer is that the averages of the columns making up C3 are more similar to those of C2 and C4 than to C1, so the dendrogram was ...
written 12 months ago by seidel7.1k
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Answer: A: how to compare the difference of read counts in a given region
... The simplest answer would be to use the Poisson distribution. Assuming your data is normalized for read depth, you have a background estimate for your window of interest (lambda = 50), and an observed count for that window in your IP (1000), so in R you could estimate this with: ppois(100, lamb ...
written 13 months ago by seidel7.1k
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Comment: C: How to create custom gtf annotation file?
... Can't you just grep for the gene name of interest and redirect the output to a file? All the lines relevant to that gene should have the ID, and this would select and place all lines with the given gene id into a single file. ...
written 16 months ago by seidel7.1k
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Comment: C: Can I compare TPM values for a transcript across different transcriptome assembl
... Yes...assuming the same set of transcripts is quantified between experiments, and the the non-zero count transcripts are identical between sets (i.e. the set of "expressed" transcripts is the same between conditions). In the case above, we both both different conditions AND different transcriptomes. ...
written 16 months ago by seidel7.1k

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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to resize a GenomicRange objects centered on a DNA motif
Scholar 8 months ago, created an answer that has been accepted. For A: How to resize a GenomicRange objects centered on a DNA motif
Appreciated 8 months ago, created a post with more than 5 votes. For C: Tabular-To-Tab Delimited Conversion
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