Moderator: seidel

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seidel6.8k
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I work as a scientist at a non-profit research institute.

Posts by seidel

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Comment: C: Seeking for a Linux based script ?
... You want to convert "15:" to ">"? Or in general, do you want to convert anything to the left of the colon, including the colon, to ">"? For any number of lines in a file? There are ways to do both. One could easily use sed, or awk, or perl, with a one-liner (so no real script required), but as ...
written 5 months ago by seidel6.8k
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Answer: A: Reproducing this plot in R
... Something like the following would work with base R functions: # make some data a <- data.frame(sample=paste0("A", 1:50), log10_total_counts=rnorm(50, 6)) # get x points x <- 1:length(a$log10_total_counts) # create plot, drop x axis plot(x, a$log10_total_cou ...
written 5 months ago by seidel6.8k
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Answer: A: Creating Count Matrix
... One suggestion using R would be: # only return file names with a given pattern dir(pattern="ReadsPerGene.out.tab") # save the results to a variable files <- dir(pattern="ReadsPerGene.out.tab") counts <- c() for( i in seq_along(files) ){ x <- read.tab ...
written 5 months ago by seidel6.8k
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Comment: C: Creating Count Matrix
... What language/method would you like to use? This can be done using shell, R, python, perl, etc.....you name it. What are you familiar with? ...
written 5 months ago by seidel6.8k
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Comment: C: RNA-Seq Differential gene expression
... One straightforward approach would be to use STAR to generate a count table that you can use with edgeR. Look up the edgeR userguide - it has a rich description of how to quantify differential gene expression given various experimental designs. ...
written 6 months ago by seidel6.8k
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Comment: C: Programmatic access to Sample Information from GEO via GSM or SRR number
... Excellent! This record has 80 samples so I can just write a loop and parse the results. There are some arguments in your example I didn't know about. Thanks! ...
written 6 months ago by seidel6.8k
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Programmatic access to Sample Information from GEO via GSM or SRR number
... How does one programmatically get access to all sample information for a given sample using either the GSM number or the SRR number? I've used esearch to get runinfo, and map from GSE series identifiers to GSM sample ids and PRJN SRA identifiers to get corresponding SRR numbers, etc. But for a given ...
geo written 6 months ago by seidel6.8k • updated 28 days ago by Biostar ♦♦ 20
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Answer: A: Perform GO analysis on genome
... I think you mean that you want to assign GO ids to the genes in your genome, as represented by the longest ORF at each locus. Correct? If so, it is common to use homology for the assignments. Find a genome that is closest to your organism - for which GO ids exist, then map your genes to that, and as ...
written 10 months ago by seidel6.8k
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Comment: C: Affymetrix Soybean Gene 1.1 ST Array PROBES IDs to Ensembl transcripts IDs
... Have you looked at the affymetrix annotation website https://www.affymetrix.com/analysis/index.affx ? They usually have both a database for looking up annotation for any probe set as well as a download section for downloading files of annotated probes (i.e. which gene /transcript ids match which pro ...
written 15 months ago by seidel6.8k
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Comment: C: ORFs extractor tool
... Can you give a little more context/information? You mean it finds ORFs in a sequence with a known error? (i.e. it would have to know the ORF sequence in advance) What are you actually trying to accomplish? ...
written 15 months ago by seidel6.8k

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