User: catglen012

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catglen0120
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Posts by catglen012

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Issue with DESeq2: Unable to create a DESeqDataSet because names in colData don'
... hello! I was able to resolve the issue by fixing how the colData is arranged. Thanks for the help nevertheless. ...
written 6 weeks ago by catglen0120
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Comment: C: Issue with DESeq2: Unable to create a DESeqDataSet because names in colData don'
... countData: gene_id Ceratodon_GG1 Ceratodon_R40 MSTRG.9134 3497 998 colData: ids sex Ceratodon_GG1 female ...
written 7 weeks ago by catglen0120
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Comment: A: Issue with creating table counts using StringTie *without* using a reference ann
... New related-question can be found here: https://www.biostars.org/p/323473/ ...
written 7 weeks ago by catglen0120
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Issue with DESeq2: Unable to create a DESeqDataSet because names in colData don't match column names in countData
... Hello! I loaded my gene(/transcript) count matrix and labels into DESeq2: > countData <- as.matrix(read.csv(file.choose(), row.names = "gene_id")) > colData <- read.table(text = readLines(file.choose(), warn = FALSE), header = TRUE, sep = "," ) But when I check that all sample ...
R deseq2 rna-seq written 7 weeks ago by catglen0120
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Comment: C: Issue with creating table counts using StringTie *without* using a reference ann
... I was able to obtain the output from prepDE.py and I was able to use this in rStudio: > countData <- as.matrix(read.csv(file.choose(), row.names = "gene_id")) > colData <- read.table(text = readLines(file.choose(), warn = FALSE), header = TRUE, sep = "," ) But when I check that ...
written 7 weeks ago by catglen0120
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Comment: C: Issue with creating table counts using StringTie *without* using a reference ann
... Hey kevin! I did the following: $ wget https://ccb.jhu.edu/software/stringtie/dl/prepDE.py --2018-06-27 10:20:20-- https://ccb.jhu.edu/software/stringtie/dl/prepDE.py Resolving ccb.jhu.edu... 128.220.233.225 Connecting to ccb.jhu.edu|128.220.233.225|:443... connected. HTTP request sent, awaiting ...
written 7 weeks ago by catglen0120
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Comment: C: Issue with creating table counts using StringTie *without* using a reference ann
... Thank you Kevin! I will download it using the script you provided. ...
written 8 weeks ago by catglen0120
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Comment: C: Issue with creating table counts using StringTie *without* using a reference ann
... It just gives me a fresh line like a "$ " usually when I encounter errors I don't get a new line that starts with $ I get "python can't find open file" ...
written 8 weeks ago by catglen0120
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Comment: C: Issue with creating table counts using StringTie *without* using a reference ann
... Nevermind, I tried finding more info about the command and the same thing appeared again. $ module load python $ module load stringtie $ find . -name "prepDE.py" $ python prepDE.py -h python: can't open file 'prepDE.py': [Errno 2] No such file or directory ...
written 8 weeks ago by catglen0120
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Comment: C: Issue with creating table counts using StringTie *without* using a reference ann
... yes! that solved the problem. Thank you Kevin. ...
written 8 weeks ago by catglen0120

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