Moderator: seidel
seidel ♦ 6.8k
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I work as a scientist at a non-profit research institute.
Posts by seidel
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... 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 6 weeks ago by
seidel ♦ 6.8k
7
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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 6 weeks ago by
seidel ♦ 6.8k
2
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2
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353
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2
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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 7 weeks ago by
seidel ♦ 6.8k
0
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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 7 weeks ago by
seidel ♦ 6.8k
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166
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... 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 9 weeks ago by
seidel ♦ 6.8k
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... 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 9 weeks ago by
seidel ♦ 6.8k
3
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2
answers
215
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2
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... 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 ...
2
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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 6 months ago by
seidel ♦ 6.8k
0
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... 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 11 months ago by
seidel ♦ 6.8k
0
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0
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278
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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 11 months ago by
seidel ♦ 6.8k
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