Moderator: seidel

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seidel7.4k
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I work as a scientist at a non-profit research institute.

Posts by seidel

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Comment: C: learning how to use Virsorter2
... First off, read the following tutorial: [How To Ask Good Questions On Technical And Scientific Forums][1] Second, read everything you can on Virsorter2. Step 3, apply your newfound knowledge until you get stuck. Then come back and ask your question, with specifics about what you're trying to do, and ...
written 5 days ago by seidel7.4k
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Comment: C: Search all SRA data for sequence? Raw reads only
... As described, your project involves finding some type of sequence that *might* exist in public SRA submissions and you'd like to scan them all to see, but this is hard. Let's say that Martians exist, I have some Martian DNA sequence, and I want to know if Martian DNA exists in any SRA submissions - ...
written 5 days ago by seidel7.4k
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Comment: C: Search all SRA data for sequence? Raw reads only
... Could you take the statistical sampling approach by considering all entries, and simply pick randomly? A queue of randomly drawn samples could be put through a pipeline, and if you expect to find something 1 in 100, or 1 in 1000, or whatever, you could get some sense for how long you'd have to run y ...
written 6 days ago by seidel7.4k
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Comment: C: Extract column which contain <20 exons in a transcript
... Translation for us mortals :) Create a subprocess to count transcripts IDs (column 4), use awk to split the id and the count and return the ID if it has a count less than 20 (print) to use as grep patterns to target lines in the original file with: -w Select only those lines containing matches tha ...
written 7 days ago by seidel7.4k
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Comment: C: Identifying cancer subtypes
... By bulk tumor data - you mean bulk RNA-Seq data from a whole tumor, correct? When you say *a* data set of whole tumor from (three tissue types) does that mean you plan to mine several sets? Will you also have matching non-cancerous tissue? If you have many data sets, some basic clustering can help y ...
written 9 days ago by seidel7.4k
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Answer: A: Does the countToFPKM package work for single end RNA seq or its only for paired
... Once you have a matrix of counts per feature, there is no way to tell if the counts for the feature came from paired-end data or single end data. The single or double endedness of your DNA Fragments is accounted for in the generation of an integer count representing a feature. Thus, your count matri ...
written 9 days ago by seidel7.4k
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Comment: C: I want to create a box plot for RNA-Seq data, but i am new to R, so i don't know
... Do you know how to make a plot of anything in R? For instance: plot(1,1)? For this question, you simply need to learn some basic R procedures. If you uncompress the file, you'll have to figure out how to read a file into R so that it's a dataframe. And then use the boxplot function to plot your data ...
written 10 days ago by seidel7.4k
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Comment: C: RNASeq datasets with different total counts
... yes, that's what I mean :) By the way, it would be interesting to see how different the experiments are by directly comparing identical samples between them. i.e. exp1Control/exp2Control. ...
written 10 days ago by seidel7.4k
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Comment: C: Compare pathway activation across microarray datasets?
... Have you tried the gene set test functions in limma? (https://rdrr.io/bioc/limma/man/geneSetTest.html) This allows you to define and score arbitrary gene sets. Thus if you have various pathways, it's an easy way to generate a score for each pathway in each data set, and maybe you can make sense of a ...
written 10 days ago by seidel7.4k
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Comment: C: RNASeq datasets with different total counts
... But edgeR and DESeq2 have normalization procedures for dealing with different sequencing depth across samples. You might simply remove genes for which you see counts in one experiment but not the other, filter further for some minimum read count across samples, and see how these methods do at identi ...
written 11 days ago by seidel7.4k

Latest awards to seidel

Scholar 9 days ago, created an answer that has been accepted. For A: How to resize a GenomicRange objects centered on a DNA motif
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Popular Question 3 months ago, created a question with more than 1,000 views. For Archiving BAM files and analysis
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Scholar 4 months ago, created an answer that has been accepted. For A: How to resize a GenomicRange objects centered on a DNA motif
Appreciated 12 months ago, created a post with more than 5 votes. For A: Technical Or Biological Replicate
Appreciated 12 months ago, created a post with more than 5 votes. For A: Entice Biologists To Learn R
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Scholar 12 months ago, created an answer that has been accepted. For A: How to resize a GenomicRange objects centered on a DNA motif
Appreciated 12 months ago, created a post with more than 5 votes. For C: Tabular-To-Tab Delimited Conversion
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Scholar 2.1 years ago, created an answer that has been accepted. For A: genomicranges outside sequence bounds
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